From pankaj at nii.res.in  Wed Feb  1 01:02:08 2006
From: pankaj at nii.res.in (Pankaj)
Date: Wed, 1 Feb 2006 11:32:08 +0530
Subject: [BiO BB] how to find gene neighbours
Message-ID: <20060201060208.M35291@nii.res.in>


Hi Everybody,
I have a few gi numbers. I want to find the their neighbouring genes. How can
I do that?

Thanking all in advance

Pankaj Khurana


--
Open WebMail Project (http://openwebmail.org)



From adarshramakumar at yahoo.co.uk  Wed Feb  1 03:20:31 2006
From: adarshramakumar at yahoo.co.uk (Adarsh Ramakumar)
Date: Wed, 1 Feb 2006 08:20:31 +0000 (GMT)
Subject: [BiO BB] how to find gene neighbours
In-Reply-To: <20060201060208.M35291@nii.res.in>
Message-ID: <20060201082031.15704.qmail@web25508.mail.ukl.yahoo.com>

Try and explore with http://string.embl.de/
It does some amazing exploration


--- Pankaj <pankaj at nii.res.in> wrote:

> 
> Hi Everybody,
> I have a few gi numbers. I want to find the their
> neighbouring genes. How can
> I do that?
> 
> Thanking all in advance
> 
> Pankaj Khurana
> 
> 
> --
> Open WebMail Project (http://openwebmail.org)
> 
> _______________________________________________
> Bioinformatics.Org general forum  - 
> BiO_Bulletin_Board at bioinformatics.org
>
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 


Mr. Adarsh Ramakumar,
BioInformatics,
University of Bremen.
http://www.biox.uni-bremen.de
Mail: adarshbiox at uni-bremen.de
Tel (W) +49-421-2182911.
Mobile   +49-1747273680.


		
___________________________________________________________ 
NEW Yahoo! Cars - sell your car and browse thousands of new and used cars online! http://uk.cars.yahoo.com/


From idoerg at gmail.com  Wed Feb  1 18:40:58 2006
From: idoerg at gmail.com (Iddo Friedberg)
Date: Wed, 01 Feb 2006 15:40:58 -0800
Subject: [BiO BB] how to find gene neighbours
In-Reply-To: <20060201060208.M35291@nii.res.in>
References: <20060201060208.M35291@nii.res.in>
Message-ID: <43E1470A.2000203@burnham.org>

Generally, you can do that by going to the genomic database of choice 
for your particular organism. As you have not mentioned which organism 
those genes are form, it is rather hard to make a recommendation. 
Ensembl, www.fruitfly.org, yeastgenome.org are examples of such 
databases for Eukaryotic models.

A list for bacterial projects is available from :

http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/genomics/bacteria.htm


HTH,

Iddo

Pankaj wrote:

>Hi Everybody,
>I have a few gi numbers. I want to find the their neighbouring genes. How can
>I do that?
>
>Thanking all in advance
>
>Pankaj Khurana
>
>
>--
>Open WebMail Project (http://openwebmail.org)
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>  
>


-- 
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Reseach
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9949
http://iddo-friedberg.org
http://BioFunctionPrediction.org



From mkgovindis at yahoo.com  Wed Feb  1 21:46:31 2006
From: mkgovindis at yahoo.com (govind mk)
Date: Wed, 1 Feb 2006 18:46:31 -0800 (PST)
Subject: [BiO BB] how to find gene neighbours
In-Reply-To: <43E1470A.2000203@burnham.org>
Message-ID: <20060202024631.50131.qmail@web34701.mail.mud.yahoo.com>

 
  I think NCBI's map viewer can elp you find neighbouring genes ..... 
  Are u looking for an algorithm or just want to map you genes on to genomes and identify their neighbours
   
  -Govind
  

Iddo Friedberg <idoerg at gmail.com> wrote:
  Generally, you can do that by going to the genomic database of choice 
for your particular organism. As you have not mentioned which organism 
those genes are form, it is rather hard to make a recommendation. 
Ensembl, www.fruitfly.org, yeastgenome.org are examples of such 
databases for Eukaryotic models.

A list for bacterial projects is available from :

http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/genomics/bacteria.htm


HTH,

Iddo

Pankaj wrote:

>Hi Everybody,
>I have a few gi numbers. I want to find the their neighbouring genes. How can
>I do that?
>
>Thanking all in advance
>
>Pankaj Khurana
>
>
>--
>Open WebMail Project (http://openwebmail.org)
>
>_______________________________________________
>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
> 
>


-- 
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Reseach
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9949
http://iddo-friedberg.org
http://BioFunctionPrediction.org

_______________________________________________
Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
  


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From pankaj at nii.res.in  Thu Feb  2 01:17:44 2006
From: pankaj at nii.res.in (Pankaj)
Date: Thu, 2 Feb 2006 11:47:44 +0530
Subject: [BiO BB] how to find gene neighbours
In-Reply-To: <20060202024631.50131.qmail@web34701.mail.mud.yahoo.com>
References: <43E1470A.2000203@burnham.org>
	<20060202024631.50131.qmail@web34701.mail.mud.yahoo.com>
Message-ID: <20060202061744.M53505@nii.res.in>


Thankx Govind!

I have gi numbers of homologous proteins from different organisms (some of
which may be sequenced and some may not be....i dont know!). I want to know
how to find gene neighbours and then automate the script to find gene
neighbours for all the gi numbers that I have. 

Pankaj Khurana

--
Open WebMail Project (http://openwebmail.org)


---------- Original Message -----------
From: govind mk <mkgovindis at yahoo.com>
To: idoerg at burnham.org, "The general forum at Bioinformatics.Org"
<bio_bulletin_board at bioinformatics.org>
Sent: Wed, 1 Feb 2006 18:46:31 -0800 (PST)
Subject: Re: [BiO BB] how to find gene neighbours

> I think NCBI's map viewer can elp you find neighbouring genes 
> .....   Are u looking for an algorithm or just want to map you genes 
> on to genomes and identify their neighbours
>    
>   -Govind
>   
> 
> Iddo Friedberg <idoerg at gmail.com> wrote:
>   Generally, you can do that by going to the genomic database of 
> choice for your particular organism. As you have not mentioned which 
> organism those genes are form, it is rather hard to make a 
> recommendation. Ensembl, www.fruitfly.org, yeastgenome.org are 
> examples of such databases for Eukaryotic models.
> 
> A list for bacterial projects is available from :
> 
> http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/genomics/bacteria.htm
> 
> HTH,
> 
> Iddo
> 
> Pankaj wrote:
> 
> >Hi Everybody,
> >I have a few gi numbers. I want to find the their neighbouring genes. How can
> >I do that?
> >
> >Thanking all in advance
> >
> >Pankaj Khurana
> >
> >
> >--
> >Open WebMail Project (http://openwebmail.org)
> >
> >_______________________________________________
> >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
> > 
> >
> 
> -- 
> Iddo Friedberg, Ph.D.
> Burnham Institute for Medical Reseach
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037 USA
> Tel: +1 (858) 646 3100 x3516
> Fax: +1 (858) 713 9949
> http://iddo-friedberg.org
> http://BioFunctionPrediction.org
> 
> _______________________________________________
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>   
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com
------- End of Original Message -------



From msr at asu.edu  Thu Feb  2 17:12:55 2006
From: msr at asu.edu (Michael S. Rosenberg)
Date: Thu, 02 Feb 2006 15:12:55 -0700
Subject: [BiO BB] Genomes, Evolution & Bioinformatics Conference
Message-ID: <43E283E7.2000208@asu.edu>

SMBE 2006 Conference (May 24 - May 28, 2006)
Genomes, Evolution & Bioinformatics
Arizona State University, Tempe, Arizona, USA

The conference will open on the evening of Wednesday, May 24
with a Welcome Social and Registration from 7:00 p.m. - 
11:00 p.m.  The opening symposia and contributed sessions 
will begin at 8:00 a.m. on May 25.  The closing symposia 
and contributed sessions will take place from 8:00 a.m.- 
12:00 noon on Sunday, May 28.  

A schedule of events at http://www.smbe.org/geb/events.htm

To register visit http://www.smbe.org/geb/registration.php
(Early registration from Feb 1 -  April 1, 2006).

Abstracts submission: http://www.smbe.org/geb/abstracts.php

For poster presentations and invited talks, we only require 
you to provide a title and authors.  For contributed talks 
and for consideration for travel awards, you need to submit
a short abstract as well. 
(Submissions accepted from Febuary 1 - March 15, 2006). 

Over 50 leading experts in Genomics, Evolutionary Biology,
and Bioinformatics have been invited and confirmed (see a 
list at http://www.smbe.org/geb/speakers).

Highlights of the scientific program at GEB2006 include:
(1) A Keynote Address every morning and over 20 invited symposia
(2) "Fitch Legacy" and "Nei Legacy" symposia celebrating
the achievements of world-renowned students and academic 
associates of Walter M. Fitch and Masatoshi Nei, 
co-founders of the journal MBE.
(3) SMBE Awards Banquet for Council Awards for 
"Life time achievement" (Dr. Tomoko Ohta) and 
"Service to Evolutionary Biology Community" (Dr. Brian Golding)
(4) A NASA Astrobiology Institute symposium on 
"Discovering the Timetree of Life"
(5) Many Graduate and Undergraduate Student Travel awards	
sponsored by SMBE (http://www.smbe.org/geb/awards.htm).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Michael S. Rosenberg, Ph.D. 
Assistant Professor
School of Life Sciences / Arizona State University 
msr at asu.edu        
http://www.public.asu.edu/~mrosenb/Lab



From wrs06 at redstar.cs.pdx.edu  Wed Feb  1 14:06:36 2006
From: wrs06 at redstar.cs.pdx.edu (wrs06 at redstar.cs.pdx.edu)
Date: Wed, 1 Feb 2006 11:06:36 -0800
Subject: [BiO BB] WRS06 1st call for paper
Message-ID: <200602011906.k11J6aKC010743@redstar.cs.pdx.edu>

[Our apologies if you receive multiple copies]
-----------------------------------------------------------------------


			      WRS06

	       The Sixth International Workshop on
	Reduction Strategies in Rewriting and Programming
	       http://www.cs.pdx.edu/~antoy/wrs06/

	      The Seattle Sheraton Hotel and Towers,
	       Seattle, Washington, August 11, 2006


Scope
    
    The workshop intends to promote and stimulate international
    research and collaboration in the area of evaluation
    strategies. It encourages the presentation of new
    directions,developments and results as well as surveys and
    tutorials on existing knowledge in this area. Reduction strategies
    study which subexpression(s) of an expression should be
    selected for evaluation and which rule(s) should be applied. These
    choices affect fundamental properties of a computation such as
    laziness, strictness, completeness and need to name a few. For this
    reason some programming languages, e.g., Elan, Maude, *OBJ* and
    Stratego, allow the explicit definition of the evaluation
    strategy, whereas other languages,e.g., Clean, Curry, and Haskell,
    allow its modification. Strategies pose challenging theoretical
    problems and play an important role in practical tools such as
    theorem provers, model checkers and programming languages. In
    implementations of languages, strategies bridge the gap between
    operational principles, e.g., graph and term rewriting,narrowing
    and lambda-calculus, and semantics, e.g., normalization,
    computation of values and head-normalization. The previous
    editions of the workshop were: WRS 2001 (Utrecht, The
    Netherlands),WRS 2002 (Copenhagen, Denmark), WRS 2003 (Valencia,
    Spain), WRS 2004 (Aachen, Germany), and WRS 2005 (Nara,
    Japan). See also the WRS permanent page at 
    http://www.dsic.upv.es/~wrs/
    
Important Dates
    
    Abstract Submission: May 8, 2006
    Paper Submission: May 15, 2006
    Author Notification: June 12, 2006
    Camera-Ready: July 10, 2006
    Conference: Aug 11, 2006
    
Program Committee
    
    Sergio Antoy, (chair) Portland State University
    Santiago Escobar, Universidad Politecnica de Valencia
    Juergen Giesl, RWTH Aachen
    Bernhard Gramlich, Technische Universitat Wien
    Ralf Laemmel, Microsoft Corp. 
    Salvador Lucas, Universidad Politecnica de Valencia
    Narciso Marti-Oliet, Universidad Complutense de Madrid
    Mizuhito Ogawa, Japan Advanced Institute of Science and Technology
    Jaco van de Pol, Centrum voor Wiskunde en Informatica
    Manfred Schmidt-Schauss, Johann Wolfgang Goethe-Universitat
    
Topics

    Topics of interest include, but are not restricted to:

    o theoretical foundations for the definition and semantic
      description of reduction strategies

    o strategies in different frameworks such as term rewriting, graph
      rewriting, infinitary rewriting, lambda calculi, higher order
      rewriting, conditional rewriting, rewriting with built-ins,
      narrowing, constraint solving, etc.

    o application of strategies to equational, functional,
      functional-logic programming languages

    o properties of reduction strategies and corresponding computations,
      e.g., completeness, computability, decidability, complexity,
      optimality, normalization, cofinality, fairness, perpetuality,
      context-freedom, need, laziness, eagerness, strictness

    o interrelations, combinations and applications of reduction under
      different strategies, e.g., evaluation mechanisms in programming
      languages, equivalence conditions for fundamental properties like
      termination and confluence, applications in modularity analysis,
      connections between strategies of different frameworks,etc.

    o program analysis and other semantics-based optimization
      techniques dealing with reduction strategies

    o rewrite systems, tools, implementations with flexible or
      programmable strategies as an essential concept or ingredient

    o specification of reduction strategies in real languages
      strategies suitable to software engineering problems and
      applications tutorials and systems related to evaluation
      strategies

Submissions

      Submissions must be original and not submitted for
      publication elsewhere. The page limit for regular papers is
      13 pages in Springer Verlag LNCS style. Surveys and
      tutorials maybe longer. Use the WRS06 submission page,
      handled by the EasyChair conference system, to submit
      abstracts, papers and to update a previous submission.

Publication

      Informal proceedings of accepted contributions will be
       available on-line. A hard copy will be distributed at the
       workshop to registered participants. Authors of
       selected contributions will be invited to submit a revised
       version, after the workshop, for inclusion in a
       collection. We anticipate the publication of formal
       proceedings in the Elsevier ENTCS series.

Contact

       Sergio Antoy, antoy at cs.pdx.edu.


From fcjooty at yahoo.com  Thu Feb  2 18:31:16 2006
From: fcjooty at yahoo.com (Franklin Jose)
Date: Thu, 2 Feb 2006 15:31:16 -0800 (PST)
Subject: [BiO BB] (no subject)
Message-ID: <20060202233116.44335.qmail@web54213.mail.yahoo.com>

  Hai everybody
  Is there any difference between tools, methods and algorithms in sequence alignment?
   
  Franklin
  Lecturer
  Govt. Arts College
  Udhagai-643002


		
---------------------------------
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From journalshoyaib at gmail.com  Fri Feb  3 06:26:03 2006
From: journalshoyaib at gmail.com (shohag md)
Date: Fri, 3 Feb 2006 17:26:03 +0600
Subject: [BiO BB] How to calculate the value of K and Lambda for two
	sequence alignment
Message-ID: <d5d467b50602030326l9e0503fma10acd31e26ec44d@mail.gmail.com>

Hi Everybody



Using Smith Waterman algorithm I want to align two sequences. Aftet that I
want to calculate the expectation value. For calculating the expectation
value we know that



E = Kmn e -lx



But how can I calculate the value of K and l .


Is there any formula that can help me to calculate the value of K and l ,  and
then the expectation value.

Thanking all in advance

Shoyaib
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From yqzhou at buffalo.edu  Fri Feb  3 08:32:30 2006
From: yqzhou at buffalo.edu (Yaoqi Zhou)
Date: Fri, 3 Feb 2006 08:32:30 -0500
Subject: [BiO BB] (no subject)
In-Reply-To: <20060202233116.44335.qmail@web54213.mail.yahoo.com>
References: <20060202233116.44335.qmail@web54213.mail.yahoo.com>
Message-ID: <f4227e4b152cdbb8213064afbe07acf3@buffalo.edu>

The most recent comparison can be found in comparing SPEM with other
sequence alignment methods.

H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment with 
sequence profiles and predicted secondary structures'', Bioinformatics 
21, 3615--3621 (2005).

Download and/or run SPEM server at http://theory.med.buffalo.edu

Yaoqi Zhou, Associate Professor
**CHECK out Newly UPDATED webpage** on
http://theory.med.buffalo.edu
Department of Physiology and Biophysics
University at Buffalo, State University of New York
124 Sherman Hall,  Buffalo, NY 14214
(716) 829-2985 Fax (716) 829-2344
Email: yqzhou at buffalo.edu
NEW Office/Lab Address: 306/308 Cary Hall

On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:

> Hai everybody
> Is there any difference between tools, methods and algorithms in 
> sequence alignment?
> ?
> Franklin
> Lecturer
> Govt. Arts College
> Udhagai-643002
>
> Relax. Yahoo! Mail virus scanning helps detect nasty 
> viruses!_______________________________________________
> Bioinformatics.Org general forum  -  
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From maximilianh at gmail.com  Fri Feb  3 09:51:19 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Fri, 3 Feb 2006 15:51:19 +0100
Subject: [BiO BB] Sequence Editor for Unix?
Message-ID: <76f031ae0602030651n7522df0dq@mail.gmail.com>

Hi,

in 2000 and 2002 someone asked on this list if there was a good
replacement for the Bioedit sequence editor for Unix. Some time has
passed from this.

So I'm asking the question again:
What are you using as a sequence editor on Linux if you have a
Biologist standing next to who who'd like to see a graphical view of
the alignment of a couple of sequences in Blast, Clustal, etc? Bioedit
could do all of this easily and quickly without any hassles.

I've tried a couple of programs. Personally, I don't like java
swing...interfaces feel rather sluggish. Apollo/Artemis take ages to
load if you just want to have a look on an alignment or run a Blast.
Strap has a strange interface. Seqpup hasn't been updated for years.
Clustalx is OK for alignment viewing can only run ClustalW.

Maybe just a small executable, C-style, that can plot blast/gff-files
and zoom, might be sufficient...

What are you using?

Thanks a lot,
Max


From pandeswati at gmail.com  Fri Feb  3 16:23:18 2006
From: pandeswati at gmail.com (Swati Pande)
Date: Fri, 3 Feb 2006 13:23:18 -0800
Subject: [BiO BB] naccess
Message-ID: <3ec517850602031323y40f213e4v569d2832c93b1e19@mail.gmail.com>

hi
I was wondering if anyone has naccess installed on linux? the problem
is that there is no way to de crypt the file on linux I tried
installing mcrypt which didnt work out and I was wondering if anyone
has had any luck with this? I really need to get naccess going.
thanks
Swati


From rwang at bccrc.ca  Fri Feb  3 17:51:31 2006
From: rwang at bccrc.ca (Renxue Wang)
Date: Fri, 3 Feb 2006 14:51:31 -0800
Subject: [BiO BB] aligment of large sequences
Message-ID: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>

Hi, there, 

Anybody knows any good program for alignment/comparison of large sequences, e.g., two genomes of closely related species, for identifying the inversion deletion and translocation. 

Thanks, 

Renxue Wang

-----Original Message-----
From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org [mailto:bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
Sent: Friday, February 03, 2006 5:33 AM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] (no subject)

The most recent comparison can be found in comparing SPEM with other
sequence alignment methods.

H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment with 
sequence profiles and predicted secondary structures'', Bioinformatics 
21, 3615--3621 (2005).

Download and/or run SPEM server at http://theory.med.buffalo.edu

Yaoqi Zhou, Associate Professor
**CHECK out Newly UPDATED webpage** on
http://theory.med.buffalo.edu
Department of Physiology and Biophysics
University at Buffalo, State University of New York
124 Sherman Hall,  Buffalo, NY 14214
(716) 829-2985 Fax (716) 829-2344
Email: yqzhou at buffalo.edu
NEW Office/Lab Address: 306/308 Cary Hall

On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:

> Hai everybody
> Is there any difference between tools, methods and algorithms in 
> sequence alignment?
> ?
> Franklin
> Lecturer
> Govt. Arts College
> Udhagai-643002
>
> Relax. Yahoo! Mail virus scanning helps detect nasty 
> viruses!_______________________________________________
> Bioinformatics.Org general forum  -  
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

_______________________________________________
Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board


From oepresearch at bellsouth.net  Fri Feb  3 19:35:05 2006
From: oepresearch at bellsouth.net (Octavio E. Pajaro)
Date: Fri, 3 Feb 2006 19:35:05 -0500
Subject: [BiO BB] naccess
In-Reply-To: <3ec517850602031323y40f213e4v569d2832c93b1e19@mail.gmail.com>
Message-ID: <20060204002638.NBHH2815.ibm62aec.bellsouth.net@masf>

I have had the same problem. I could never decrypt the program. 
Octavio

-----Original Message-----
From:
bio_bulletin_board-bounces+oepresearch=bellsouth.net at bioinformatics.org
[mailto:bio_bulletin_board-bounces+oepresearch=bellsouth.net at bioinformatics.
org] On Behalf Of Swati Pande
Sent: Friday, February 03, 2006 4:23 PM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] naccess

hi
I was wondering if anyone has naccess installed on linux? the problem
is that there is no way to de crypt the file on linux I tried
installing mcrypt which didnt work out and I was wondering if anyone
has had any luck with this? I really need to get naccess going.
thanks
Swati
_______________________________________________
Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From hamid at ibb.ut.ac.ir  Sat Feb  4 02:15:07 2006
From: hamid at ibb.ut.ac.ir (hamid)
Date: Sat, 04 Feb 2006 10:45:07 +0330
Subject: [BiO BB] aligment of large sequences
In-Reply-To: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
References: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
Message-ID: <WorldClient-F200602041045.AA45070011@ibb.ut.ac.ir>

 Dear Wang,
 Mummer is a suitable program for this reason. Note that this program only 
runs on Unix base OSs.
 Yours,
 Hamid

/*
 Hamid Nikbakht,
 M.Sc of Cell and Molecular Biology,
 Laboratory of Biophysics and Molecular Biology,
 Bioinformatics Department,
 Institute of Biochemistry and Biophysics(IBB),
 University of Tehran,
 Tehran,Iran.
 Tel: +98-21-6111-3322
 Fax: +98-21-640-4680
 E-Mail: hamid at ibb.ut.ac.ir
 Alt. E-mail: nikbakht at ibb.ut.ac.ir
*/




From william.hsiao at gmail.com  Sat Feb  4 03:15:51 2006
From: william.hsiao at gmail.com (William Hsiao)
Date: Sat, 4 Feb 2006 00:15:51 -0800
Subject: [BiO BB] aligment of large sequences
In-Reply-To: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
References: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
Message-ID: <679a35b20602040015y8595febif95a80e740474b88@mail.gmail.com>

Hi Renxue,
   You might want to try http://gel.ahabs.wisc.edu/mauve/

Cheers,

Will

On 2/3/06, Renxue Wang <rwang at bccrc.ca> wrote:
> Hi, there,
>
> Anybody knows any good program for alignment/comparison of large sequences, e.g., two genomes of closely related species, for identifying the inversion deletion and translocation.
>
> Thanks,
>
> Renxue Wang
>
> -----Original Message-----
> From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org [mailto:bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
> Sent: Friday, February 03, 2006 5:33 AM
> To: The general forum at Bioinformatics.Org
> Subject: Re: [BiO BB] (no subject)
>
> The most recent comparison can be found in comparing SPEM with other
> sequence alignment methods.
>
> H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment with
> sequence profiles and predicted secondary structures'', Bioinformatics
> 21, 3615--3621 (2005).
>
> Download and/or run SPEM server at http://theory.med.buffalo.edu
>
> Yaoqi Zhou, Associate Professor
> **CHECK out Newly UPDATED webpage** on
> http://theory.med.buffalo.edu
> Department of Physiology and Biophysics
> University at Buffalo, State University of New York
> 124 Sherman Hall,  Buffalo, NY 14214
> (716) 829-2985 Fax (716) 829-2344
> Email: yqzhou at buffalo.edu
> NEW Office/Lab Address: 306/308 Cary Hall
>
> On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:
>
> > Hai everybody
> > Is there any difference between tools, methods and algorithms in
> > sequence alignment?
> >
> > Franklin
> > Lecturer
> > Govt. Arts College
> > Udhagai-643002
> >
> > Relax. Yahoo! Mail virus scanning helps detect nasty
> > viruses!_______________________________________________
> > Bioinformatics.Org general forum  -
> > BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>


--
William Hsiao
PhD Student, Brinkman Laboratory
Department of Molecular Biology and Biochemistry
Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6
Phone: 604-291-4206 Fax: 604-291-5583


From boris.steipe at utoronto.ca  Sat Feb  4 09:04:11 2006
From: boris.steipe at utoronto.ca (Boris Steipe)
Date: Sat, 4 Feb 2006 09:04:11 -0500
Subject: [BiO BB] aligment of large sequences
In-Reply-To: <679a35b20602040015y8595febif95a80e740474b88@mail.gmail.com>
References: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
	<679a35b20602040015y8595febif95a80e740474b88@mail.gmail.com>
Message-ID: <90E9EEE7-5A13-43CB-9F8E-3FAD12EEBD20@utoronto.ca>

You could also try LAGAN

http://lagan.stanford.edu/lagan_web/index.shtml

in particular Shuffle_Lagan handles inversions, transpositions(!) and  
even some degree of duplications.

HTH,

B.




On 4 Feb 2006, at 03:15, William Hsiao wrote:

> Hi Renxue,
>    You might want to try http://gel.ahabs.wisc.edu/mauve/
>
> Cheers,
>
> Will
>
> On 2/3/06, Renxue Wang <rwang at bccrc.ca> wrote:
>> Hi, there,
>>
>> Anybody knows any good program for alignment/comparison of large  
>> sequences, e.g., two genomes of closely related species, for  
>> identifying the inversion deletion and translocation.
>>
>> Thanks,
>>
>> Renxue Wang
>>
>> -----Original Message-----
>> From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org  
>> [mailto:bio_bulletin_board-bounces 
>> +rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
>> Sent: Friday, February 03, 2006 5:33 AM
>> To: The general forum at Bioinformatics.Org
>> Subject: Re: [BiO BB] (no subject)
>>
>> The most recent comparison can be found in comparing SPEM with other
>> sequence alignment methods.
>>
>> H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment  
>> with
>> sequence profiles and predicted secondary structures'',  
>> Bioinformatics
>> 21, 3615--3621 (2005).
>>
>> Download and/or run SPEM server at http://theory.med.buffalo.edu
>>
>> Yaoqi Zhou, Associate Professor
>> **CHECK out Newly UPDATED webpage** on
>> http://theory.med.buffalo.edu
>> Department of Physiology and Biophysics
>> University at Buffalo, State University of New York
>> 124 Sherman Hall,  Buffalo, NY 14214
>> (716) 829-2985 Fax (716) 829-2344
>> Email: yqzhou at buffalo.edu
>> NEW Office/Lab Address: 306/308 Cary Hall
>>
>> On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:
>>
>>> Hai everybody
>>> Is there any difference between tools, methods and algorithms in
>>> sequence alignment?
>>>
>>> Franklin
>>> Lecturer
>>> Govt. Arts College
>>> Udhagai-643002
>>>
>>> Relax. Yahoo! Mail virus scanning helps detect nasty
>>> viruses!_______________________________________________
>>> Bioinformatics.Org general forum  -
>>> BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>
>
> --
> William Hsiao
> PhD Student, Brinkman Laboratory
> Department of Molecular Biology and Biochemistry
> Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada  
> V5A 1S6
> Phone: 604-291-4206 Fax: 604-291-5583
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From sravan_111 at rediffmail.com  Mon Feb  6 05:46:51 2006
From: sravan_111 at rediffmail.com (sravan  sravan)
Date: 6 Feb 2006 10:46:51 -0000
Subject: [BiO BB] (no subject)
Message-ID: <20060206104651.28130.qmail@webmail10.rediffmail.com>

Dear friends,
             I am working to study microsatellites. In this regard, I have to generate the 
equivalent classes of repeat motifs. Hence, I request for your assistance by providing me 
the source code, methodology or algorithm in detail / pseudo code. 
Ex: AA,AC,AG,AT,CA,CC,CG,CT,GA,GC,GG,GT,TA,TC,TG,TT :
            AC : AC,CA,GT,TG
            AG : AG,GA,CT,TG
------------------------------------------------------------------
In addition: For Tri,Tetra,Penta,Hexa Motifs:
                Ex: ACG,CGA,GAC      AGC,GCA,CAG should be in two seperate classes. But I am 
getting in single class due to the equal nucleotide composition. Please suggest me some 
solution for this and any additional issues explored by you.

          I appreciate your early response, as it is an urgent requirement.
 
Thank you very much.

Regads.
Sravan. ?

Dear Bio_Bulletin_Board,
               This is an urgent requirement. Hence, I request for your early response.

Thanks.
Sravan.
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From narcis at fiserlab.org  Mon Feb  6 11:29:41 2006
From: narcis at fiserlab.org (Narcis Fernandez-Fuentes)
Date: Mon, 06 Feb 2006 11:29:41 -0500
Subject: [BiO BB] naccess
In-Reply-To: <20060204002638.NBHH2815.ibm62aec.bellsouth.net@masf>
References: <20060204002638.NBHH2815.ibm62aec.bellsouth.net@masf>
Message-ID: <43E77975.9050606@fiserlab.org>


I think you should contact naccess authors'


Octavio E. Pajaro wrote:
> I have had the same problem. I could never decrypt the program. 
> Octavio
> 
> -----Original Message-----
> From:
> bio_bulletin_board-bounces+oepresearch=bellsouth.net at bioinformatics.org
> [mailto:bio_bulletin_board-bounces+oepresearch=bellsouth.net at bioinformatics.
> org] On Behalf Of Swati Pande
> Sent: Friday, February 03, 2006 4:23 PM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] naccess
> 
> hi
> I was wondering if anyone has naccess installed on linux? the problem
> is that there is no way to de crypt the file on linux I tried
> installing mcrypt which didnt work out and I was wondering if anyone
> has had any luck with this? I really need to get naccess going.
> thanks
> Swati
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> 
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 

-- 


From lato4864 at uidaho.edu  Mon Feb  6 12:27:03 2006
From: lato4864 at uidaho.edu (Andrew Latos)
Date: Mon, 06 Feb 2006 09:27:03 -0800
Subject: [BiO BB] naccess
In-Reply-To: <43E77975.9050606@fiserlab.org>
References: <20060204002638.NBHH2815.ibm62aec.bellsouth.net@masf>
	<43E77975.9050606@fiserlab.org>
Message-ID: <f4f483c93cce2.3cce2f4f483c9@uidaho.edu>

Hi there,
  you get the decryption key from your registration.  Then you use your
decryption software in linux to read it.  It took me a couple of tries
to find the right combination but eventually it will work.

cheers,
Andrew L

:-)

----- Original Message -----
From: Narcis Fernandez-Fuentes <narcis at fiserlab.org>
Date: Monday, February 6, 2006 8:30 am
Subject: Re: [BiO BB] naccess
To: "The general forum at Bioinformatics.Org"
<bio_bulletin_board at bioinformatics.org>

> 
> I think you should contact naccess authors'
> 
> 
> Octavio E. Pajaro wrote:
> > I have had the same problem. I could never decrypt the program. 
> > Octavio
> > 
> > -----Original Message-----
> > From:
> > bio_bulletin_board-
> bounces+oepresearch=bellsouth.net at bioinformatics.org> 
>
[mailto:bio_bulletin_board-bounces+oepresearch=bellsouth.net at bioinformatics.
> > org] On Behalf Of Swati Pande
> > Sent: Friday, February 03, 2006 4:23 PM
> > To: bio_bulletin_board at bioinformatics.org
> > Subject: [BiO BB] naccess
> > 
> > hi
> > I was wondering if anyone has naccess installed on linux? the 
> problem> is that there is no way to de crypt the file on linux I tried
> > installing mcrypt which didnt work out and I was wondering if anyone
> > has had any luck with this? I really need to get naccess going.
> > thanks
> > Swati
> > _______________________________________________
> > Bioinformatics.Org general forum  -  
> BiO_Bulletin_Board at bioinformatics.org> 
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board> 
> > 
> > _______________________________________________
> > Bioinformatics.Org general forum  -  
> BiO_Bulletin_Board at bioinformatics.org> 
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board> 
> 
> -- 
> _______________________________________________
> Bioinformatics.Org general forum  -  
>
BiO_Bulletin_Board at bioinformatics.orghttps://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 


From rwang at bccrc.ca  Mon Feb  6 13:24:25 2006
From: rwang at bccrc.ca (Renxue Wang)
Date: Mon, 6 Feb 2006 10:24:25 -0800
Subject: [BiO BB] aligment of large sequences
Message-ID: <0BE438149FF2254DB4199E2682C8DFEB702975@crcmail1.BCCRC.CA>

Thanks so much. :) Renxue

-----Original Message-----
From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org
[mailto:bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org] On
Behalf Of Boris Steipe
Sent: Saturday, February 04, 2006 6:04 AM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] aligment of large sequences

You could also try LAGAN

http://lagan.stanford.edu/lagan_web/index.shtml

in particular Shuffle_Lagan handles inversions, transpositions(!) and  
even some degree of duplications.

HTH,

B.




On 4 Feb 2006, at 03:15, William Hsiao wrote:

> Hi Renxue,
>    You might want to try http://gel.ahabs.wisc.edu/mauve/
>
> Cheers,
>
> Will
>
> On 2/3/06, Renxue Wang <rwang at bccrc.ca> wrote:
>> Hi, there,
>>
>> Anybody knows any good program for alignment/comparison of large  
>> sequences, e.g., two genomes of closely related species, for  
>> identifying the inversion deletion and translocation.
>>
>> Thanks,
>>
>> Renxue Wang
>>
>> -----Original Message-----
>> From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org  
>> [mailto:bio_bulletin_board-bounces 
>> +rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
>> Sent: Friday, February 03, 2006 5:33 AM
>> To: The general forum at Bioinformatics.Org
>> Subject: Re: [BiO BB] (no subject)
>>
>> The most recent comparison can be found in comparing SPEM with other
>> sequence alignment methods.
>>
>> H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment  
>> with
>> sequence profiles and predicted secondary structures'',  
>> Bioinformatics
>> 21, 3615--3621 (2005).
>>
>> Download and/or run SPEM server at http://theory.med.buffalo.edu
>>
>> Yaoqi Zhou, Associate Professor
>> **CHECK out Newly UPDATED webpage** on
>> http://theory.med.buffalo.edu
>> Department of Physiology and Biophysics
>> University at Buffalo, State University of New York
>> 124 Sherman Hall,  Buffalo, NY 14214
>> (716) 829-2985 Fax (716) 829-2344
>> Email: yqzhou at buffalo.edu
>> NEW Office/Lab Address: 306/308 Cary Hall
>>
>> On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:
>>
>>> Hai everybody
>>> Is there any difference between tools, methods and algorithms in
>>> sequence alignment?
>>>
>>> Franklin
>>> Lecturer
>>> Govt. Arts College
>>> Udhagai-643002
>>>
>>> Relax. Yahoo! Mail virus scanning helps detect nasty
>>> viruses!_______________________________________________
>>> Bioinformatics.Org general forum  -
>>> BiO_Bulletin_Board at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>
>
> --
> William Hsiao
> PhD Student, Brinkman Laboratory
> Department of Molecular Biology and Biochemistry
> Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada  
> V5A 1S6
> Phone: 604-291-4206 Fax: 604-291-5583
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

_______________________________________________
Bioinformatics.Org general forum  -
BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board


From pandeswati at gmail.com  Mon Feb  6 13:54:27 2006
From: pandeswati at gmail.com (Swati Pande)
Date: Mon, 6 Feb 2006 10:54:27 -0800
Subject: [BiO BB] naccess:problem solved
Message-ID: <3ec517850602061054g2ec17f20kc0e7cbf64ebe125e@mail.gmail.com>

Hi
I managed to install it. You need mcrypt for this and I just had a
friend who had mcrypt installed on Ubuntu to de-crypt it for me.
thanks so much
Swati


From maximilianh at gmail.com  Tue Feb  7 06:50:31 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Tue, 7 Feb 2006 12:50:31 +0100
Subject: [BiO BB] aligment of large sequences
In-Reply-To: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
References: <0BE438149FF2254DB4199E2682C8DFEB702971@crcmail1.BCCRC.CA>
Message-ID: <76f031ae0602070350y2766ef3as@mail.gmail.com>

UCSC is using Blastz for the actual alignment and TBA for the postprocessing.

http://www.bx.psu.edu/miller_lab/

Max

On 03/02/06, Renxue Wang <rwang at bccrc.ca> wrote:
> Hi, there,
>
> Anybody knows any good program for alignment/comparison of large sequences, e.g., two genomes of closely related species, for identifying the inversion deletion and translocation.
>
> Thanks,
>
> Renxue Wang
>
> -----Original Message-----
> From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org [mailto:bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
> Sent: Friday, February 03, 2006 5:33 AM
> To: The general forum at Bioinformatics.Org
> Subject: Re: [BiO BB] (no subject)
>
> The most recent comparison can be found in comparing SPEM with other
> sequence alignment methods.
>
> H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment with
> sequence profiles and predicted secondary structures'', Bioinformatics
> 21, 3615--3621 (2005).
>
> Download and/or run SPEM server at http://theory.med.buffalo.edu
>
> Yaoqi Zhou, Associate Professor
> **CHECK out Newly UPDATED webpage** on
> http://theory.med.buffalo.edu
> Department of Physiology and Biophysics
> University at Buffalo, State University of New York
> 124 Sherman Hall,  Buffalo, NY 14214
> (716) 829-2985 Fax (716) 829-2344
> Email: yqzhou at buffalo.edu
> NEW Office/Lab Address: 306/308 Cary Hall
>
> On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:
>
> > Hai everybody
> > Is there any difference between tools, methods and algorithms in
> > sequence alignment?
> >
> > Franklin
> > Lecturer
> > Govt. Arts College
> > Udhagai-643002
> >
> > Relax. Yahoo! Mail virus scanning helps detect nasty
> > viruses!_______________________________________________
> > Bioinformatics.Org general forum  -
> > BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>


--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler


From bioinfosm at gmail.com  Tue Feb  7 12:16:10 2006
From: bioinfosm at gmail.com (Samantha Fox)
Date: Tue, 7 Feb 2006 12:16:10 -0500
Subject: [BiO BB] Updating NCBI databases
Message-ID: <726450810602070916g2f525b20rae9b09f7183e4209@mail.gmail.com>

Hi,
I had a question regarding regular update of BLAST databases. Is there a
standard way to move the updated databases to the user section, making sure
that the current copy is not already in use ?

Suppose I update the database monthly, but a user might have a big BLAST job
running when my cron script starts the update. This can lead to errors. How
can I prevent that ?

Thanks,
 ~S
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From areed at imdc.org  Tue Feb  7 12:45:16 2006
From: areed at imdc.org (Ann Reed)
Date: Tue, 7 Feb 2006 11:45:16 -0600
Subject: [BiO BB] Education: Tuition-free on-line bioinformatics training
	program seeks students
Message-ID: <7BDF6464945AB045B845C2AB588B9B401B88AB@204.21.125.209.transedge.com>

	BiTmaP: Midwest Bioinformatics Training Program, is seeking students for the semester that begins in May 2006. All tuition and course materials are paid for by a generous grant from the U.S. Dept. of Labor. 
	
	BiTmaP courses are accredited and provided by the University of Illinois at Chicago (UIC). Our program consists of on-line lectures, industry seminars and work-site and internship experiences that focus on standard bioinformatics principles and protocols used widely throughout industry and academia. 
	
	Students complete 3 of the following 4 courses and earn 12-graduate level credits and a certificate in bioinformatics from UIC. BiTmaP courses are: Introduction to Bioinformatics, Biostatistics, Functional Computational Genomics and Microarray, Molecular Modeling in Bioinformatics.
	To pre-qualify for training, send a resume or CV to apply at bitmapchicago.com
	For more information, please visit http://www.bitmapchicago.com or email Program Director, Ann Reed at areed at bitmapchicago.com



From b.d.vanschaik at amc.uva.nl  Wed Feb  8 06:40:16 2006
From: b.d.vanschaik at amc.uva.nl (Barbera van Schaik)
Date: Wed, 08 Feb 2006 12:40:16 +0100
Subject: [BiO BB] 3rd International Symposium on Networks in Bioinformatics
Message-ID: <43E9D8A0.1080002@amc.uva.nl>

*/3rd International Symposium on Networks in Bioinformatics/*
29, 30 and 31 may 2006
Amsterdam, the Netherlands
http://isnb.amc.uva.nl/
 
Deadline for abstract submission: 1 april 2006
Early-bird registration: before 1 april 2006
* *
*/Symposium focus: Bioinformatics of networks/*
Bioinformatics of biological networks involves a range of interconnected 
multidisciplinary research topics. Research areas include the 
quantitative understanding of the dynamics of regulatory and metabolic 
networks by using modeling and simulation techniques, the reconstruction 
of biological pathways from experimental data, identification of pathway 
modules, the analysis and interpretation of experimental data in the 
context of biological networks, the construction and use of (public) 
pathway databases, network visualization and the development and use of 
pathway markup languages such as SBML and BioPax. Biological questions 
and new experimental techniques as well as ongoing (bio)informatics and 
statistics efforts will guide the development of the next generation of 
bioinformatics software packages. The combination of computational and 
genomics research will accelerate the detailed understanding of 
biological networks, which will find many applications in all 
application domains of life sciences.
*/ /*
*/Bridging the gap between disciplines/*
ISNB is specifically aimed at researchers working in life sciences, 
which includes disciplines like molecular biology, genomics, 
bioinformatics, biostatistics, informatics, computational life sciences 
and mathematical biology. Since more and more researchers are focusing 
on biological networks from different perspectives there is large 
interest in a dedicated symposium like the ISNB. ISNB provides a 
platform to bring together these different researchers in this field to 
exchange ideas and facilitate new national and international 
collaborations. Experience from ISNB2004 and ISNB2005 learns that there 
is a significant interest in this symposium. This symposium will also 
contribute to merge ideas and research from scientific programs in the 
field of bioinformatics, computational life sciences (e.g. simulation 
and modeling) and the experimental genomics work.
 
*/Scientific program and tutorial lectures/*
The Third International Symposium on Networks in Bioinformatics (ISNB 
2006) is likely to continue its success from previous years by bringing 
together different disciplines to discuss ongoing research in this 
exciting field of biological networks and bioinformatics. In 
continuation of ISNB 2005 we aim to organize a three day meeting during 
which we will again schedule a mix of tutorial lectures and scientific 
presentations. The scientific program includes research and poster 
presentations from Dutch and international acknowledged researchers but 
also from young researchers starting in the field. The tutorial lectures 
provide an excellent opportunity to have well known researchers in the 
field give an introduction to junior and senior researchers and students 
who recently started working in related projects. The setup of the 
symposium facilitates sufficient possibilities to meet and talk to 
colleague researchers, which will facilitate many new and exciting 
collaborations and research projects.
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From joel.dudley at asu.edu  Wed Feb  8 15:24:27 2006
From: joel.dudley at asu.edu (Joel Dudley)
Date: Wed, 8 Feb 2006 13:24:27 -0700
Subject: [BiO BB] MacResearch.org announces iPod giveaway contest
Message-ID: <23FF1B53-F91F-434B-8DD8-05D936A1E55E@asu.edu>

Help MacResearch.org expand its Script Repository and you could win a  
black 2GB iPod Nano. Eligible contestants must submit a research- 
oriented script that can run natively (no emulators) on Mac OS X 10.3  
or higher without modification before the contest end date. Scripts  
for all scientific domains are welcome including scripts written for  
High Performance Computing (grid, cluster, etc) setup and management.  
If your script does not meet the aforementioned criteria then you  
will not be eligible to win the iPod Nano. Winners will be chosen by  
random drawing. The contest begins 2/8/2006 and ends 2/28/2006.  The  
ultimate goal of this contest, and the script repository in general,  
is to create a valuable community resource that can be used to  
benefit endeavors in research and education. Please don't be shy  
about your coding style or lack of documentation. Your script will  
make someone's life easier. To learn more about MacResearch.org and  
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From jeff at bioinformatics.org  Wed Feb  8 18:46:40 2006
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Wed, 08 Feb 2006 18:46:40 -0500
Subject: [BiO BB] Fwd: Call for Papers2006 Summer Computer Simulation
	Conference (SCSC'06)
Message-ID: <43EA82E0.2070209@bioinformatics.org>

Call for Papers2006 Summer Computer Simulation Conference (SCSC'06)
July 30- August 3, 2006Coast Plaza HotelCalgary, Alberta, Canada
http://www.scs.org/confernc/summersim/summersim06/cfp/scsc06.htm

Track: 			Bioinformatics
Track chair: 		Isaac Barjis
Affiliation:		New York City College of TechnologyCity University of New York
Contac:	Email: ibarjis at cityech.cuny.edu; Tel.: (718) 260-5285; Fax: (718) 254-8680

Introduction
The Bioinformatics track is organized within the SCSC and aims at understanding 
living systems through studying and retrieving biological information using 
computational methods, approaches, computer tools and graphics. Although 
Bioinformatics is an established subject, its study and investigation are 
exposing more and more challenges, perspectives and opportunities. Results of 
the studies in this field have profound impacts on all fields of biology as a 
subject, development of science in general, and wealth of human society and 
health. This fascinating new field of research requires valuable research 
efforts and therefore you are invited to consider this track for discussion and 
publication of your outstanding research works. Although the track welcomes all 
related works, authors are especially encouraged to submit their original 
research findings on the topics suggested below.

Suggested Topics:
1) Systems Biology Modeling & Simulation?	
2) Protein Structure Prediction and Modeling?	
3) Medical Informatics?	
4) Chemical/Molecular Bioinformatics ?	
5) Metabolic Pathways?	
6) Gene Identification, Annotation and Expression		
7) Biological Data Mining, Modeling & Integration?	
8) Pharmacogenetics and Pharmacogenomics?	
9) Analysis of Evolution and Phylogeny?	
10) Biological Data Visualization?	

Important Dates:
Full Draft Paper/Extended Abstract: 	March 15, 2006
Preliminary Notification of Acceptance: 	May 2, 2006
Final Camera Ready Submission Due: 	May 23, 2006

Please submit the extended abstract (4-6 pages) as a PDF file via 
http://mc.manuscriptcentral.com/scsc  (New users, please create an account 
first: to create an account, on the mentioned site, click on "Create Account" 
in the left hand upper corner)

Dr. I. Barjis
Assistant Professor
Department of Physical and Biological Sciences
Room P313
300 Jay Street
Brooklyn, NY 11201

Phone: (718)2605285
Fax: (718)2548680
Fax: (718) 254-8595 Department Office
http://websupport1.citytech.cuny.edu/Faculty/ibarjis



From golharam at umdnj.edu  Wed Feb  8 23:41:05 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Wed, 08 Feb 2006 23:41:05 -0500
Subject: [BiO BB] Updating NCBI databases
In-Reply-To: <726450810602070916g2f525b20rae9b09f7183e4209@mail.gmail.com>
Message-ID: <003101c62d33$0ac480b0$e6028a0a@GOLHARMOBILE1>

I think the easiest way is to do a 'ps -ef | grep blast'.  If it returns
a process (other than itself) in the list, then you know someone is
running blast.  
 
The other (simpler) option is to maintain a seperate BLAST database that
you can copy in place under a standard maintainence window.  We normally
reboot our server once a month when system patches are applied.  During
this outage period, the new database could be copied in place.
 
Let me know what you end up doing.  I'm curious to the solution you
decide on.  I might want to use that here.  
 
Ryan
 
 
-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of Samantha Fox
Sent: Tuesday, February 07, 2006 12:16 PM
To: The general forum at Bioinformatics.Org
Subject: [BiO BB] Updating NCBI databases



Hi,
I had a question regarding regular update of BLAST databases. Is there a
standard way to move the updated databases to the user section, making
sure that the current copy is not already in use ?

Suppose I update the database monthly, but a user might have a big BLAST
job running when my cron script starts the update. This can lead to
errors. How can I prevent that ?

Thanks,
~S 

-------------- next part --------------
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From golharam at umdnj.edu  Wed Feb  8 23:46:43 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Wed, 08 Feb 2006 23:46:43 -0500
Subject: [BiO BB] Tool to mutate DNA sequence
Message-ID: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>

Does anyone know of tool to mutate a DNA sequence by a specified amount?
For instance, say I have a DNA sequence 1000 bases long, and I want to
simulate mutations to make it 75% (or 80%, etc) similar to the original.


Ryan



From pmr at ebi.ac.uk  Thu Feb  9 03:25:24 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Thu, 9 Feb 2006 08:25:24 -0000 (GMT)
Subject: [BiO BB] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <2714.86.132.216.50.1139473524.squirrel@webmail.ebi.ac.uk>

Ryan Golhar writes:

> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.

EMBOSS has the msbar program ("mutate sequence beyond all recognition")
which allows you to select the number and type of changes.

With some tuning of options to match the sequence length you should be
able to get results that match whatever your definition of 75% similar
might be (amazing how much more similarity you can get by adding gaps in
an alignment :-)

If you can specify a clear and generally useful way to define what you
need we could of course add a "percent change" option to the msbar program
for a future release.

Hope that helps,

Peter



From torsten.seemann at infotech.monash.edu.au  Thu Feb  9 06:15:28 2006
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 09 Feb 2006 22:15:28 +1100
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <43EB2450.6000606@infotech.monash.edu.au>

Ryan,

> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.

The EMBOSS suite comes with a tool called "msbar" which can controllably 
mutate sequences:

http://emboss.sourceforge.net/apps/msbar.html

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/


From heikki at sanbi.ac.za  Thu Feb  9 06:31:20 2006
From: heikki at sanbi.ac.za (Heikki Lehvaslaiho)
Date: Thu, 9 Feb 2006 13:31:20 +0200
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <200602091331.21690.heikki@sanbi.ac.za>

Ryan,

Instructions in pseudo code:

take the sequence string out of the object
use a hash to store changed locations
repeat 
    pick a location in the string randomly
    if the location is not in a hash , i.e. changed already, 
        change it into something else
    add the changed location into the hash
    if enough locations have been changed (scalar keys hash), exit loop
put the sequence string back into the seq object

   -Heikki   

On Thursday 09 February 2006 06:46, Ryan Golhar wrote:
> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.
>
>
> Ryan
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


From osborne1 at optonline.net  Thu Feb  9 08:55:57 2006
From: osborne1 at optonline.net (Brian Osborne)
Date: Thu, 09 Feb 2006 08:55:57 -0500
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <C010B41D.72BE%osborne1@optonline.net>

Ryan,

The script scripts/utilities/mutate.PLS does this.

Brian O.


On 2/8/06 11:46 PM, "Ryan Golhar" <golharam at umdnj.edu> wrote:

> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.
> 
> 
> Ryan
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From heikki at sanbi.ac.za  Thu Feb  9 09:54:30 2006
From: heikki at sanbi.ac.za (Heikki Lehvaslaiho)
Date: Thu, 9 Feb 2006 16:54:30 +0200
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <200602091654.30890.heikki@sanbi.ac.za>

Ryan,

I should have made this very clear in my first reply:

You have to plan very carefully what rules you use when you mutate your 
sequence because it will affect directly the resulting sequences. Of course,  
all that depends on what you will be using the sequences for. If you are 
going to draw evolutionary conclusions from those sequences, you must mutate 
them in a way that simulates evolutionary principles.

My earlier pseudocode example, for example, should allow mutations in every 
location. Mutations do occur multiple times in same places as sequences get 
saturated by mutations. Also, you should decide the relative occurrence of 
transversions versus transitions. Then there are indels; do you want to take 
those into account?

Also, check the EMBOSS program 'msbar'.

You did not ask this, but... I remember that during the early days of Celera, 
one of the tools that enabled them to estimate the feasibility of the whole 
genome shotgun sequence assembly, was a very complete program to 'synthesize' 
in-silico the whole complexity of the human genome. I have no idea of that 
program is generally available now.

Yours,

    -Heikki

On Thursday 09 February 2006 06:46, Ryan Golhar wrote:
> Does anyone know of tool to mutate a DNA sequence by a specified amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the original.
>
>
> Ryan
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


From jeff at bioinformatics.org  Thu Feb  9 12:17:44 2006
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Thu, 09 Feb 2006 12:17:44 -0500
Subject: [BiO BB] New features for hosted projects
Message-ID: <43EB7938.2010801@bioinformatics.org>

Greetings,

Bioinformatics.Org is pleased to announce a couple recent additions to the 
services offered to projects hosted at Bioinformatics.Org.

1. Subversion (SVN) version control system

Software developers may now use the Subversion version control system on our 
servers.  Subversion was developed "to take over the CVS user base," according 
to the Subversion website.  "Specifically, we're writing a new version control 
system that is very similar to CVS, but fixes many things that are broken." 
Here are a few of the advantages of using Subversion over CVS (from the website):

     * Directories, renames, and file meta-data are versioned.
     * Commits are truly atomic.
     * Versioning of symbolic links
     * Efficient handling of binary files

Subversion at Bioinformatics.Org makes use of svnserve over SSH (svn+ssh) for 
developer access (anonymous access uses ordinary svnserve).  Instructions on 
using Subversion at BiO can be found here:

     http://bioinformatics.org/docs/svn/

We also have the WebSVN interface set up:

     http://bioinformatics.org/websvn/

2. Wiki system for project websites

Bioinformatics.Org will now install a wiki system in project web directories by 
default.  If you're not familiar with wikis, you may want to look through this 
introduction by Wikipedia:

     http://en.wikipedia.org/wiki/Wiki

Instructions for using wikis and the wiki system are also included with (are 
part of) the website.

Some projects are just getting started using their new wikis, so there's not 
much content to show at this time, but an example of the system can be seen here:

     http://bioinformatics.org/dnalinux/

More information on Bioinformatics.Org's free group-hosting service can be 
found here:

     http://bioinformatics.org/about/hosting.php

If you have any questions or comments, please don't hesitate to ask:

     sysadmins at bioinformatics.org

Cheers,
Jeff
-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600
--


From jason.stajich at duke.edu  Thu Feb  9 14:10:54 2006
From: jason.stajich at duke.edu (Jason Stajich)
Date: Thu, 9 Feb 2006 14:10:54 -0500
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <0B84EE38-0BA5-4E56-B35F-C8CBAA342AC4@duke.edu>

Depending on whether or not you want to use evolutionary realistic  
models...
* evolver which comes with PAML lets you evolve sequences on a tree
* SeqGen from Andrew Rambaut http://evolve.zoo.ox.ac.uk/software.html? 
id=seqgen
also lets you do this
I believe there are PISE interfaces to both of these at the pasteur  
bioweb site - http://bioweb.pasteur.fr/

-jason
On Feb 8, 2006, at 11:46 PM, Ryan Golhar wrote:

> Does anyone know of tool to mutate a DNA sequence by a specified  
> amount?
> For instance, say I have a DNA sequence 1000 bases long, and I want to
> simulate mutations to make it 75% (or 80%, etc) similar to the  
> original.
>
>
> Ryan
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12




From marksty at MIT.EDU  Thu Feb  9 15:00:24 2006
From: marksty at MIT.EDU (Mark Styczynski)
Date: Thu, 09 Feb 2006 15:00:24 -0500
Subject: [BiO BB] Old versions of Prosite?
Message-ID: <1139515224.9315.21.camel@localhost>

Hi,

I'm looking to replicate the results from an earlier work that used
PROSITE version 8.0.  I wrote to the email contact on ExPASy, and I was
told that though things like Swiss-Prot have old versions archived,
older versions of PROSITE are considered as obsolete and no longer
available to users.  I've tried scraping Google but have yet to get
anything as old as what I'm looking for.

Does anyone have any old versions of PROSITE, or have any idea how I
could get access to them?  

Thanks for any help you can give,
Mark Styczynski



From golharam at umdnj.edu  Thu Feb  9 16:19:46 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Thu, 09 Feb 2006 16:19:46 -0500
Subject: [BiO BB] RE: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <200602091654.30890.heikki@sanbi.ac.za>
Message-ID: <002801c62dbe$8d4d7e20$e6028a0a@GOLHARMOBILE1>

Thanks all.  The responses I got were definitely more than helpful.  FYI
- I did initially look at msbar.  I glanced over the "Number of times to
perform mutation operations", which is what I was looking for.  

I'm looking to statistically test some simply scoring matrices.  I think
msbar will do.

Ryan

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Heikki
Lehvaslaiho
Sent: Thursday, February 09, 2006 9:55 AM
To: bioperl-l at lists.open-bio.org; golharam at umdnj.edu
Cc: 'The general forum at Bioinformatics.Org'; 'bioperl-l';
emboss at emboss.open-bio.org
Subject: Re: [Bioperl-l] Tool to mutate DNA sequence


Ryan,

I should have made this very clear in my first reply:

You have to plan very carefully what rules you use when you mutate your 
sequence because it will affect directly the resulting sequences. Of
course,  
all that depends on what you will be using the sequences for. If you are

going to draw evolutionary conclusions from those sequences, you must
mutate 
them in a way that simulates evolutionary principles.

My earlier pseudocode example, for example, should allow mutations in
every 
location. Mutations do occur multiple times in same places as sequences
get 
saturated by mutations. Also, you should decide the relative occurrence
of 
transversions versus transitions. Then there are indels; do you want to
take 
those into account?

Also, check the EMBOSS program 'msbar'.

You did not ask this, but... I remember that during the early days of
Celera, 
one of the tools that enabled them to estimate the feasibility of the
whole 
genome shotgun sequence assembly, was a very complete program to
'synthesize' 
in-silico the whole complexity of the human genome. I have no idea of
that 
program is generally available now.

Yours,

    -Heikki

On Thursday 09 February 2006 06:46, Ryan Golhar wrote:
> Does anyone know of tool to mutate a DNA sequence by a specified 
> amount? For instance, say I have a DNA sequence 1000 bases long, and I

> want to simulate mutations to make it 75% (or 80%, etc) similar to the

> original.
>
>
> Ryan
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From pankaj at nii.res.in  Fri Feb 10 01:43:13 2006
From: pankaj at nii.res.in (Pankaj)
Date: Fri, 10 Feb 2006 12:13:13 +0530
Subject: [BiO BB] how to find gene neighbours
In-Reply-To: <1139334677.43e8de159cb95@webservices.di.fc.ul.pt>
References: <43E1470A.2000203@burnham.org>
	<20060202024631.50131.qmail@web34701.mail.mud.yahoo.com>
	<20060202061744.M53505@nii.res.in>
	<1139334677.43e8de159cb95@webservices.di.fc.ul.pt>
Message-ID: <20060210064313.M41802@nii.res.in>


Hi Pooja,
Nops!
By gene neighbours I mean genes which are positionally close together on the
genome, ie adjoining genes.
Although I found the NCBI's map viewer friendly, but I couldnt figure out how
 to automate a script which can find gene neighbours for all the GI's that I
have. Presently, having a GI number I can find gene neighbours manually by
looking at the chromosome map, but I dont know how data is organised in the
database, so that I can automate the process.
Any help on this will be highly appreciated!
Cheers,
Pankaj Khurana

--
Open WebMail Project (http://openwebmail.org)


---------- Original Message -----------
From: Pooja Jain <pjain at xldb.di.fc.ul.pt>
To: pankaj at nii.res.in
Sent: Tue,  7 Feb 2006 17:51:17 +0000
Subject: Re: [BiO BB] how to find gene neighbours

> Hi,
> Probably u will be interested in idetifying the set of GI numbers 
> from the GI number you have which share evolutionaly relationship. 
> In other words you are trying to find genes from different organisms 
> which are neighbours during their parallel evolution. Am I 
> understood you correctly ?
> 
> cheers!
> 
> -Pooja
> Citando Pankaj <pankaj at nii.res.in>:
> 
> >
> > Thankx Govind!
> >
> > I have gi numbers of homologous proteins from different organisms (some of
> > which may be sequenced and some may not be....i dont know!). I want to know
> > how to find gene neighbours and then automate the script to find gene
> > neighbours for all the gi numbers that I have.
> >
> > Pankaj Khurana
> >
> > --
> > Open WebMail Project (http://openwebmail.org)
> >
> >
> > ---------- Original Message -----------
> > From: govind mk <mkgovindis at yahoo.com>
> > To: idoerg at burnham.org, "The general forum at Bioinformatics.Org"
> > <bio_bulletin_board at bioinformatics.org>
> > Sent: Wed, 1 Feb 2006 18:46:31 -0800 (PST)
> > Subject: Re: [BiO BB] how to find gene neighbours
> >
> > > I think NCBI's map viewer can elp you find neighbouring genes
> > > .....   Are u looking for an algorithm or just want to map you genes
> > > on to genomes and identify their neighbours
> > >
> > >   -Govind
> > >
> > >
> > > Iddo Friedberg <idoerg at gmail.com> wrote:
> > >   Generally, you can do that by going to the genomic database of
> > > choice for your particular organism. As you have not mentioned which
> > > organism those genes are form, it is rather hard to make a
> > > recommendation. Ensembl, www.fruitfly.org, yeastgenome.org are
> > > examples of such databases for Eukaryotic models.
> > >
> > > A list for bacterial projects is available from :
> > >
> > >
> > http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/genomics/bacteria.htm
> > >
> > > HTH,
> > >
> > > Iddo
> > >
> > > Pankaj wrote:
> > >
> > > >Hi Everybody,
> > > >I have a few gi numbers. I want to find the their neighbouring genes. How
> > can
> > > >I do that?
> > > >
> > > >Thanking all in advance
> > > >
> > > >Pankaj Khurana
> > > >
> > > >
> > > >--
> > > >Open WebMail Project (http://openwebmail.org)
> > > >
> > > >_______________________________________________
> > > >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> > > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > > >
> > > >
> > > >
> > > >
> > >
> > > --
> > > Iddo Friedberg, Ph.D.
> > > Burnham Institute for Medical Reseach
> > > 10901 N. Torrey Pines Rd.
> > > La Jolla, CA 92037 USA
> > > Tel: +1 (858) 646 3100 x3516
> > > Fax: +1 (858) 713 9949
> > > http://iddo-friedberg.org
> > > http://BioFunctionPrediction.org
> > >
> > > _______________________________________________
> > > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > >
> > >
> > > __________________________________________________
> > > Do You Yahoo!?
> > > Tired of spam?  Yahoo! Mail has the best spam protection around
> > > http://mail.yahoo.com
> > ------- End of Original Message -------
> >
> > _______________________________________________
> > Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
------- End of Original Message -------



From kiekyon.huang at gmail.com  Fri Feb 10 05:31:37 2006
From: kiekyon.huang at gmail.com (Kie Kyon Huang)
Date: Fri, 10 Feb 2006 18:31:37 +0800
Subject: [BiO BB] (no subject)
Message-ID: <a54400840602100231i203305ech99c9fa4e6dbb0ebf@mail.gmail.com>


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From delete at elfdata.com  Fri Feb 10 09:13:29 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Fri, 10 Feb 2006 14:13:29 +0000
Subject: [BiO BB] Understanding Smith-Waterman scoring
Message-ID: <F87B8D52-2FD7-496D-8559-412391431FCD@elfdata.com>

Hi people,

I'm trying to learn about Smith-Waterman. There is one thing I  
haven't seen answered in explanations of the Smith-Waterman algorithm.

How does it score alignments that come in sections? Does it give a  
penalty if a sequence must be split up?

For example, let's say I had the protein AAAABBBB, and I wanted to  
see how this scored against the protein BBBBAAAA. Let's ignore the  
fact that it can be reversed, for the moment, just so I can  
understand how should Smith-Waterman work.

Now, what would the match score be? Let's assume that A to A has a  
score of 1 and B to B also has a score of 1. Its a really simple  
example. So matching AAAABBBB to itself, would give a SW score of 8.

What would matching BBBBAAAA to AAAABBBB give?

I'd expect it to generate two "sections", like this:

AAAA
::::
AAAA

BBBB
::::
BBBB


But what should the overall score be? Is it still 8? Or should we  
give a penalty because we've had to split this up? Is it normal for  
alignment tools to give penalties to segmented sequences. Also is  
there some kind of "minimum length" that a Smith-Waterman based  
aligner would allow? Would it say that you can't have sections below  
a certain length? Are there any tools which let you specify such a  
minimum section length?


If you don't like that example above of AAAABBBB (as it can be  
reversed), then try this example. Assume all the proteins get a score  
of 1 against themselves. The protein: ABCDEFGH, if I did a Smith- 
Waterman score comparison against DCHABGEF, would the score still be  
8. After all, all the proteins are there, just in a different order.

I would expect this to get a score of zero or below.


It's a really basic question, sorry about that!





From pmr at ebi.ac.uk  Fri Feb 10 09:22:39 2006
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 10 Feb 2006 14:22:39 +0000
Subject: [BiO BB] Understanding Smith-Waterman scoring
In-Reply-To: <F87B8D52-2FD7-496D-8559-412391431FCD@elfdata.com>
References: <F87B8D52-2FD7-496D-8559-412391431FCD@elfdata.com>
Message-ID: <43ECA1AF.2020206@ebi.ac.uk>

Theodore H. Smith wrote:

> How does it score alignments that come in sections? Does it give a  
> penalty if a sequence must be split up?

You get one alignment.

If more than one "section" aligns ... with the parts in the same order in both 
proteins ... you can have a misaligned region and/or gaps in the sequences. 
There are penalty scores for the misalignments and the gaps.

There is also a Smith-Waterman-Eggert variation of the algorithm that finds a 
scond, third, fourth ... alignment that excludes all those already reported.

Smith-Waterman is a local alignment method, so any unaligned parts of either 
sequence do not count in the score.


> What would matching BBBBAAAA to AAAABBBB give?

AAAA matching AAAA or BBBB matching BBBB (unless A has a positive score to 
match B, then other results are possible)

> I'd expect it to generate two "sections", like this:

No, but you will get the second section from the Smith-Waterman-Eggert 
algorithm. Each will have its own local alignment score.

> But what should the overall score be? Is it still 8? Or should we  give 
> a penalty because we've had to split this up? Is it normal for  
> alignment tools to give penalties to segmented sequences. Also is  there 
> some kind of "minimum length" that a Smith-Waterman based  aligner would 
> allow? Would it say that you can't have sections below  a certain 
> length? Are there any tools which let you specify such a  minimum 
> section length?

> If you don't like that example above of AAAABBBB (as it can be  
> reversed), then try this example. Assume all the proteins get a score  
> of 1 against themselves. The protein: ABCDEFGH, if I did a Smith- 
> Waterman score comparison against DCHABGEF, would the score still be  8. 
> After all, all the proteins are there, just in a different order.
> 
> I would expect this to get a score of zero or below.

Be careful not to confuse protein (the whole sequence) with amino acid or 
residue (one character).

You will get at least 1 residue matching. Maybe more as some of the mismatches 
will have a positive score.

Hope that helps. It is cmoplicated :-)

Peter



From delete at elfdata.com  Fri Feb 10 09:53:18 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Fri, 10 Feb 2006 14:53:18 +0000
Subject: [BiO BB] Understanding Smith-Waterman scoring
In-Reply-To: <43ECA1AF.2020206@ebi.ac.uk>
References: <F87B8D52-2FD7-496D-8559-412391431FCD@elfdata.com>
	<43ECA1AF.2020206@ebi.ac.uk>
Message-ID: <B0390116-7BC8-4DA6-8CC0-1465F418D4EA@elfdata.com>


On 10 Feb 2006, at 14:22, Peter Rice wrote:

> Theodore H. Smith wrote:
>
>> How does it score alignments that come in sections? Does it give  
>> a  penalty if a sequence must be split up?
>
> You get one alignment.
>
> If more than one "section" aligns ... with the parts in the same  
> order in both proteins ... you can have a misaligned region and/or  
> gaps in the sequences. There are penalty scores for the  
> misalignments and the gaps.

OK. I understand. The most popular tools in use today, only find the  
best (or at least one) locally aligned section, but not all of them.

Is this a problem in general? Or is it that multiple sections to be  
aligned, are quite rare in the kind of queries that biologists do today?

> There is also a Smith-Waterman-Eggert variation of the algorithm  
> that finds a scond, third, fourth ... alignment that excludes all  
> those already reported.

Am I right in seeing that this isn't talked about as much as Smith- 
Waterman though? It sounds promising for the line of work I am doing  
however, thanks very much for telling me of Smith-Waterman-Eggert, it  
looks like a good lead.

>> What would matching BBBBAAAA to AAAABBBB give?
>
> AAAA matching AAAA or BBBB matching BBBB (unless A has a positive  
> score to match B, then other results are possible)

Which would I get? Does it depend on the tool? Do I get the first  
alignment, the last, or the best?

>> I'd expect it to generate two "sections", like this:
>
> No, but you will get the second section from the Smith-Waterman- 
> Eggert algorithm. Each will have its own local alignment score.

Thanks. Sounds very interesting.

>> But what should the overall score be? Is it still 8? Or should we   
>> give a penalty because we've had to split this up? Is it normal  
>> for  alignment tools to give penalties to segmented sequences.  
>> Also is  there some kind of "minimum length" that a Smith-Waterman  
>> based  aligner would allow? Would it say that you can't have  
>> sections below  a certain length? Are there any tools which let  
>> you specify such a  minimum section length?
>
>> If you don't like that example above of AAAABBBB (as it can be   
>> reversed), then try this example. Assume all the proteins get a  
>> score  of 1 against themselves. The protein: ABCDEFGH, if I did a  
>> Smith- Waterman score comparison against DCHABGEF, would the score  
>> still be  8. After all, all the proteins are there, just in a  
>> different order.
>> I would expect this to get a score of zero or below.
>
> Be careful not to confuse protein (the whole sequence) with amino  
> acid or residue (one character).

You might not be surprised to find out that I come from a software  
developer background. I won't make that mistake again.

> You will get at least 1 residue matching. Maybe more as some of the  
> mismatches will have a positive score.
>
> Hope that helps. It is cmoplicated :-)

Yes it's been of great help. And yes it is complicated :)





From pmr at ebi.ac.uk  Fri Feb 10 12:32:32 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Fri, 10 Feb 2006 17:32:32 -0000 (GMT)
Subject: [BiO BB] Understanding Smith-Waterman scoring
In-Reply-To: <B0390116-7BC8-4DA6-8CC0-1465F418D4EA@elfdata.com>
References: <F87B8D52-2FD7-496D-8559-412391431FCD@elfdata.com>
	<43ECA1AF.2020206@ebi.ac.uk>
	<B0390116-7BC8-4DA6-8CC0-1465F418D4EA@elfdata.com>
Message-ID: <3475.86.137.129.90.1139592752.squirrel@webmail.ebi.ac.uk>

>> Theodore H. Smith wrote:
> OK. I understand. The most popular tools in use today, only find the
> best (or at least one) locally aligned section, but not all of them.
>
> Is this a problem in general? Or is it that multiple sections to be
> aligned, are quite rare in the kind of queries that biologists do today?

The algorithm guarantees one alignment, and it is always the "best"
(highest scoring) ... although in your AAAABBBB case there arer two
possible answers with the same score. Changing the comparison matrix
(scores for A:A, B:B and A:B) and changing the penalties for adding gaps
will of course change the scoring and may give another "best" alignment.

There is also the closely related Needleman-Wunsch global alignment
algorithm. This guarantees one best alignment over the whole of both
sequences. In global alignment there are usually options to penalise gaps
at the end of the sequence (usually not penalised as both sequences arer
assumed to be incomplete). In local alignments (Smith-Waterman) the
alignment is what you get ... there are no penalties for anything outside
the aligned regions (except that edxtending the alignment will always give
a worse score).

>> There is also a Smith-Waterman-Eggert variation of the algorithm
>> that finds a scond, third, fourth ... alignment that excludes all
>> those already reported.
>
> Am I right in seeing that this isn't talked about as much as Smith-
> Waterman though? It sounds promising for the line of work I am doing
> however, thanks very much for telling me of Smith-Waterman-Eggert, it
> looks like a good lead.

SMith-Waterman is standard. There are utilities that give the alternative
but often users fail to spot the possibility. The first alignment is
always the same for both.

> You might not be surprised to find out that I come from a software
> developer background. I won't make that mistake again.

Ah, in that case be careful what you describe as a "sequence" ...
mathematicians can have different ideas of what the word means :-)

>> You will get at least 1 residue matching. Maybe more as some of the
>> mismatches will have a positive score.

regards,

Peter Rice



From golharam at umdnj.edu  Sat Feb 11 01:25:50 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 11 Feb 2006 01:25:50 -0500
Subject: [BiO BB] Understanding Smith-Waterman scoring
In-Reply-To: <B0390116-7BC8-4DA6-8CC0-1465F418D4EA@elfdata.com>
Message-ID: <001b01c62ed4$01ca08c0$2f01a8c0@GOLHARMOBILE1>

Theodore,

Smith-Waterman will find all the alignments.  Remember, a mismatch must
have a negative score.  Once the aligned region drops to 0, the end of
the alignment is reached.  

A second area alignment is found by looking at the matrix of scores it
generated and locating the next highest score. You can then trace back
along the diagonal until you get zero at which point you reached the end
of the next alignment.

Ryan

-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of Theodore H. Smith
Sent: Friday, February 10, 2006 9:53 AM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] Understanding Smith-Waterman scoring



On 10 Feb 2006, at 14:22, Peter Rice wrote:

> Theodore H. Smith wrote:
>
>> How does it score alignments that come in sections? Does it give
>> a  penalty if a sequence must be split up?
>
> You get one alignment.
>
> If more than one "section" aligns ... with the parts in the same
> order in both proteins ... you can have a misaligned region and/or  
> gaps in the sequences. There are penalty scores for the  
> misalignments and the gaps.

OK. I understand. The most popular tools in use today, only find the  
best (or at least one) locally aligned section, but not all of them.

Is this a problem in general? Or is it that multiple sections to be  
aligned, are quite rare in the kind of queries that biologists do today?

> There is also a Smith-Waterman-Eggert variation of the algorithm
> that finds a scond, third, fourth ... alignment that excludes all  
> those already reported.

Am I right in seeing that this isn't talked about as much as Smith- 
Waterman though? It sounds promising for the line of work I am doing  
however, thanks very much for telling me of Smith-Waterman-Eggert, it  
looks like a good lead.

>> What would matching BBBBAAAA to AAAABBBB give?
>
> AAAA matching AAAA or BBBB matching BBBB (unless A has a positive
> score to match B, then other results are possible)

Which would I get? Does it depend on the tool? Do I get the first  
alignment, the last, or the best?

>> I'd expect it to generate two "sections", like this:
>
> No, but you will get the second section from the Smith-Waterman-
> Eggert algorithm. Each will have its own local alignment score.

Thanks. Sounds very interesting.

>> But what should the overall score be? Is it still 8? Or should we   
>> give a penalty because we've had to split this up? Is it normal
>> for  alignment tools to give penalties to segmented sequences.  
>> Also is  there some kind of "minimum length" that a Smith-Waterman  
>> based  aligner would allow? Would it say that you can't have  
>> sections below  a certain length? Are there any tools which let  
>> you specify such a  minimum section length?
>
>> If you don't like that example above of AAAABBBB (as it can be   
>> reversed), then try this example. Assume all the proteins get a
>> score  of 1 against themselves. The protein: ABCDEFGH, if I did a  
>> Smith- Waterman score comparison against DCHABGEF, would the score  
>> still be  8. After all, all the proteins are there, just in a  
>> different order.
>> I would expect this to get a score of zero or below.
>
> Be careful not to confuse protein (the whole sequence) with amino
> acid or residue (one character).

You might not be surprised to find out that I come from a software  
developer background. I won't make that mistake again.

> You will get at least 1 residue matching. Maybe more as some of the
> mismatches will have a positive score.
>
> Hope that helps. It is cmoplicated :-)

Yes it's been of great help. And yes it is complicated :)



_______________________________________________
Bioinformatics.Org general forum  -
BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From golharam at umdnj.edu  Sat Feb 11 01:21:26 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 11 Feb 2006 01:21:26 -0500
Subject: [BiO BB] How to calculate the value of K and Lambda for two
	sequence alignment
In-Reply-To: <d5d467b50602030326l9e0503fma10acd31e26ec44d@mail.gmail.com>
Message-ID: <001601c62ed3$637d6fe0$2f01a8c0@GOLHARMOBILE1>

Did anyone ever respond to you on this?  K and lambda.  I forget where K
comes from.  Lambda is dependent on the scoring matrix you are using.  I
believe it is given with the matrix.  BLOSUM uses 0.347.
 
Ryan
 

-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of shohag md
Sent: Friday, February 03, 2006 6:26 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] How to calculate the value of K and Lambda for two
sequence alignment



Hi Everybody

 

Using Smith Waterman algorithm I want to align two sequences. Aftet that
I want to calculate the expectation value. For calculating the
expectation value we know that 

 

E = Kmn e - lx

 

But how can I calculate the value of K and l .

 

Is there any formula that can help me to calculate the value of K and l
,  and then the expectation value.
 
Thanking all in advance

Shoyaib


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From journalshoyaib at gmail.com  Sun Feb 12 06:36:15 2006
From: journalshoyaib at gmail.com (shohag md)
Date: Sun, 12 Feb 2006 17:36:15 +0600
Subject: [BiO BB] How to calculate the value of k and lambda for calculating
	the expectation value?
Message-ID: <d5d467b50602120336k121e399cv4e6707b279a859a1@mail.gmail.com>

Hi everybody



After aligning two/more sequences I want to find the expectation value.

But for calculating the expectation value we know that there are two
constanats, k and lambda.(E= kmn e-lambda *s, where m and n are the lengths
of sequences)

Now I want to know how to calculate the value of k and lambda.

I want to know the mathematics , not any tool .



Are there any one who can help me?

Thanks in advance



shoyaib
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From maximilianh at gmail.com  Sun Feb 12 07:50:53 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Sun, 12 Feb 2006 13:50:53 +0100
Subject: [BiO BB] How to calculate the value of K and Lambda for two
	sequence alignment
In-Reply-To: <001601c62ed3$637d6fe0$2f01a8c0@GOLHARMOBILE1>
References: <d5d467b50602030326l9e0503fma10acd31e26ec44d@mail.gmail.com>
	<001601c62ed3$637d6fe0$2f01a8c0@GOLHARMOBILE1>
Message-ID: <76f031ae0602120450n6206f0d6t@mail.gmail.com>

I have no clue :-) but I typed "smith waterman k lamda" into google
and clicked on "I'm feeling lucky":

got the NCBI page where blast is explained
http://www.people.virginia.edu/~wrp/cshl02/Altschul/Altschul-3.html:

---------------
K and lambda are statistical parameters dependent upon the scoring
system and the background amino acid frequences of the sequences being
compared. While FASTA estimates these parameters from the scores
generated by actual database searches, BLAST estimates them beforehand
for specific scoring schemes by comparing many random sequences
generated using a standard protein amino acid composition [12].
   For example, using BLOSUM-62 amino acid substitution scores [13],
and affine gap costs [14-16] in which a gap of length k is assigned a
score of -(10 + k), we generated 10,000 pairs of length-1000 random
protein sequences, and used the Smith-Waterman algorithm to calculate
10,000 optimal local alignment scores. From these scores, lambda was
estimated at 0.252 and K at 0.035 by the method of maximum-likelihood
[17]. In general, given M samples from an extreme value distribution,
the ratio of the maximum-likelihood estimate of lambda to its actual
value is approximately normally distributed, with mean 1.0 and
standard deviation 0.78/sqrt(M) [17]. Thus the standard error for our
estimate of lambda is about 0.002, or less than 1%.
---------------

>From what I understood, you generate many alignments, plot the
generated scores for the current matrix, assume that they follow your
function E and then approximate lambda.

The addison wesley BLAST book goes into details and gives an example
PERL program to calculate lambda and says that the value of k doesn't
really matter:
(this sample chapter is free)
http://www.oreilly.com/catalog/blast/chapter/ch04.pdf

Don't know if it helped or if it is completelywrong, it took 10
minutes and I found it interesting... :-)

Max


On 11/02/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> Did anyone ever respond to you on this?  K and lambda.  I forget where K
> comes from.  Lambda is dependent on the scoring matrix you are using.  I
> believe it is given with the matrix.  BLOSUM uses 0.347.
>
> Ryan
>
>
> -----Original Message-----
> From:
> bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
> [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org]
> On Behalf Of shohag md
> Sent: Friday, February 03, 2006 6:26 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] How to calculate the value of K and Lambda for two
> sequence alignment
>
>
>
> Hi Everybody
>
>
>
> Using Smith Waterman algorithm I want to align two sequences. Aftet that I
> want to calculate the expectation value. For calculating the expectation
> value we know that
>
>
>
> E = Kmn e - lx
>
>
>
> But how can I calculate the value of K and l .
>
>
> Is there any formula that can help me to calculate the value of K and l ,
> and then the expectation value.
>
> Thanking all in advance
>
> Shoyaib
>
> _______________________________________________
> Bioinformatics.Org general forum  -
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>


--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler


From delete at elfdata.com  Mon Feb 13 17:45:10 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Mon, 13 Feb 2006 22:45:10 +0000
Subject: [BiO BB] Constructing a multiple aligner, similar to Smith-Waterman
Message-ID: <70024952-5394-48F6-8402-902186876C6B@elfdata.com>

Hi people,

I am trying to figure out how to construct my own multiple aligner.  
Not because I expect it to be better than other aligners, but because  
I need to learn about alignment for a larger project. I need to get  
this all figured out.

I know that when aligning a Smith-Waterman based aligner, we start  
from the highest cell in the matrix, and trace backwards. But what if  
the trace actually has multiple highest cells? Or what if it goes  
like this:

13, 11, 13, 10, 9, 6, 3, 1, 0

That is, the trace has multiple highest cells within it, two 13's. Do  
we use the shorter back trace?

OK, so let's assume we got a single alignment done. How do we then  
find the other sections to align? Would a process of elimination do  
it? That is, search the remaining matrix (Excluding the portion  
already aligned) for the highest cell?

All this Smith-Waterman understanding I'm gaining is going into go  
into an experimental project I am working on, that I have no idea if  
it will be practical or not. I know it will work, I just don't know  
that it will give anyone any benefits over what they already got :)  
Needless to say, it's exciting stuff for people like me who like  
giving something new a go, I suppose the danger of it not being  
useful is half the excitement.




From pmr at ebi.ac.uk  Tue Feb 14 03:20:25 2006
From: pmr at ebi.ac.uk (pmr at ebi.ac.uk)
Date: Tue, 14 Feb 2006 08:20:25 -0000 (GMT)
Subject: [BiO BB] Constructing a multiple aligner,
	similar to Smith-Waterman
In-Reply-To: <70024952-5394-48F6-8402-902186876C6B@elfdata.com>
References: <70024952-5394-48F6-8402-902186876C6B@elfdata.com>
Message-ID: <4425.86.137.129.90.1139905225.squirrel@webmail.ebi.ac.uk>


> That is, the trace has multiple highest cells within it, two 13's. Do
> we use the shorter back trace?

There is nothing special about either score. You should choose the first
or last one you see (whichever is easiest). Usually there is very little
difference between them, although I have seen perfect repeats in proteins
which would each align with a single repeat in another sequence :-)

> OK, so let's assume we got a single alignment done. How do we then
> find the other sections to align? Would a process of elimination do
> it? That is, search the remaining matrix (Excluding the portion
> already aligned) for the highest cell?

Yes, that's how Smith-Waterman-Eggert works. Check the original paper for
the rules (if memory serves, zero all cells that contributed to the
previous alignment and then look for the highest remainning score)

One thing nconcerns me a little ... you mentioned "multiple alignment".
Local (Smith-Waterman) alignments will do the best matches, but you need a
strategy for the remainder of each sequence. Depending on your project
this could be anything from a global alignment to throwing the rest away
(alignments looking for protein domains do this, for example).

Hope this helps,

Peter



From maximilianh at gmail.com  Tue Feb 14 05:11:42 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Tue, 14 Feb 2006 11:11:42 +0100
Subject: [BiO BB] Re: [Bioperl-l] Tool to mutate DNA sequence
In-Reply-To: <0B84EE38-0BA5-4E56-B35F-C8CBAA342AC4@duke.edu>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<0B84EE38-0BA5-4E56-B35F-C8CBAA342AC4@duke.edu>
Message-ID: <76f031ae0602140211n2a0bbf4fl@mail.gmail.com>

The tool ROSE also evolves sequences on a tree. There is a web
interface and downloadable source at
http://bibiserv.techfak.uni-bielefeld.de/rose/

Max

On 09/02/06, Jason Stajich <jason.stajich at duke.edu> wrote:
> Depending on whether or not you want to use evolutionary realistic
> models...
> * evolver which comes with PAML lets you evolve sequences on a tree
> * SeqGen from Andrew Rambaut http://evolve.zoo.ox.ac.uk/software.html?
> id=seqgen
> also lets you do this
> I believe there are PISE interfaces to both of these at the pasteur
> bioweb site - http://bioweb.pasteur.fr/
>
> -jason
> On Feb 8, 2006, at 11:46 PM, Ryan Golhar wrote:
>
> > Does anyone know of tool to mutate a DNA sequence by a specified
> > amount?
> > For instance, say I have a DNA sequence 1000 bases long, and I want to
> > simulate mutations to make it 75% (or 80%, etc) similar to the
> > original.
> >
> >
> > Ryan
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>


--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler


From jeff at bioinformatics.org  Wed Feb 15 18:49:59 2006
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Wed, 15 Feb 2006 18:49:59 -0500
Subject: [BiO BB] Bioinformatics.Org announces the laureate of the 2006
 Benjamin Franklin Award
Message-ID: <43F3BE27.9040001@bioinformatics.org>

Bioinformatics.Org is proud to present the 2006 Benjamin Franklin Award in the 
Life Sciences to Michael Ashburner of Cambridge University.  As expressed by 
his nominators, Prof. Ashburner has made fundamental contributions to many open 
access bioinformatics projects including FlyBase [1], the GASP project [2], the 
Gene Ontology project [3], and the Open Biological Ontologies project [4], and 
he was instrumental in the establishment of the European Bioinformatics 
Institute [5]. He is also known for advocating open access to biological 
information [6].

The Benjamin Franklin Award in the Life Sciences is a humanitarian award 
presented annually by Bioinformatics.Org to an individual who has, in his or 
her practice, promoted free and open access to the materials and methods used 
in the life sciences.  The Award is named for Benjamin Franklin (1706-1790), 
one of the most remarkable men of his time.  Scientist, inventor, statesman, 
Franklin freely and openly shared his ideas and refused to patent his 
inventions, and it is the opinion of the founders of Bioinformatics.Org that he 
embodied the best traits of a scientist.

At the end of 2005, requests for nominations for the 2006 Award were sent out 
to more than 17,000 members of Bioinformatics.Org.  Any individual who received 
more than one nomination was considered a nominee and had their name placed on 
the ballot for final selection by the membership.

The ceremony for the presentation of the Award will be held at the 2006 
Bioinformatics.Org Annual Meeting (BiOAM), held in conjunction with the Life 
Sciences Conference and Expo, Boston, Massachusetts, April 3 to 5, 2006.  The 
presentation will be made April 5 at 10:00 AM, and it is open to all attendees. 
  It involves a short introduction, the presentation of the certificate, and 
the laureate seminar.  Please see http://bio-itworldexpo.com/ for more 
information on the event.

Past laureates of the Benjamin Franklin Award in the Life Sciences include Ewan 
Birney (2005), Lincoln Stein (2004), James Kent (2003) and Michael Eisen 
(2002).  More information on the Award can be found at 
http://bioinformatics.org/franklin/.

References:
1. http://www.flybase.org/
2. http://www.fruitfly.org/GASP1/
3. http://www.geneontology.org/
4. http://obo.sourceforge.net/
5. http://www.ebi.ac.uk/
6. http://www.newscientist.com/article.ns?id=dn2061



From maithreyi_roses at yahoo.co.in  Wed Feb 15 11:02:16 2006
From: maithreyi_roses at yahoo.co.in (maithreyi thaticherla)
Date: Wed, 15 Feb 2006 16:02:16 +0000 (GMT)
Subject: [BiO BB] What exactly the clustering of DNA means?
Message-ID: <20060215160216.6863.qmail@web8414.mail.in.yahoo.com>

Hi
  This is Maithreyi , studying final B.Tech . Iam doing a project on Clustering a DNA sequence.
  Iam a computer student so iam not having knowledge on this bioinformatics.But iam interested to know how is this DNA present in our body. 
  My doubt is how can we cluster a DNA sequence.Iam using k-means algorithm and iam unable to link this algorithm with my topic.
  I want to know the exact steps of k-means algorithm with Clustering of DNA sequences.
  Can anyone help me immediately plz.
  k bye

				
---------------------------------
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
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From ykalidas at gmail.com  Thu Feb 16 11:07:15 2006
From: ykalidas at gmail.com (Kalidas Yeturu)
Date: Thu, 16 Feb 2006 21:37:15 +0530
Subject: [BiO BB] What exactly the clustering of DNA means?
In-Reply-To: <20060215160216.6863.qmail@web8414.mail.in.yahoo.com>
References: <20060215160216.6863.qmail@web8414.mail.in.yahoo.com>
Message-ID: <5632703b0602160807h7b781074ha17f808bcc2bf69f@mail.gmail.com>

you may want to check out BLAST program suite to know how DNA sequences will
be approximately compared. It gives a score (called Z score) which you can
use it as clustering threshold. and mean of a cluster you can define as that
dna sequence which is similar to most of the sequences. If you do not want
approximate approach for clustering, you can use pairwise sequence alignment
algorithms (smith waterman/Hidden markov model-approach) when you have not
many sequences to cluster.



On 2/15/06, maithreyi thaticherla <maithreyi_roses at yahoo.co.in> wrote:
>
> Hi
> This is Maithreyi , studying final B.Tech . Iam doing a project on
> Clustering a DNA sequence.
> Iam a computer student so iam not having knowledge on this
> bioinformatics.But iam interested to know how is this DNA present in our
> body.
> My doubt is how can we cluster a DNA sequence.Iam using k-means algorithm
> and iam unable to link this algorithm with my topic.
> I want to know the exact steps of k-means algorithm with Clustering of DNA
> sequences.
> Can anyone help me immediately plz.
> k bye
>
> ------------------------------
> Jiyo cricket on Yahoo! India cricket<http://us.rd.yahoo.com/mail/in/mailcricket/*http://in.sports.yahoo.com/cricket/>
> Yahoo! Messenger Mobile<http://us.rd.yahoo.com/mail/in/mailmobilemessenger/*http://in.mobile.yahoo.com/new/messenger/>Stay in touch with your buddies all the time.
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>


--
Kalidas Y
http://ssl.serc.iisc.ernet.in/~kalidas
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From delete at elfdata.com  Thu Feb 16 16:43:10 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Thu, 16 Feb 2006 21:43:10 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
Message-ID: <1F3D43D3-4C57-4145-B255-DF12A579A4A7@elfdata.com>

Hi people,

I've installed blast on my computer. I'm getting some errors using a  
custom DB.

ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
ShatterProof% blastall -p blastp -d customgene.txt -i query.txt -o  
result.out

[NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
[NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill  
returned non-zero status
[NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.


however, this example copied from ncbi's website, works just fine:

ShatterProof% cd /usr/blast/dbs/
ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out

I get a text file containing the result.

Is that because I'm using blastp in the first attempt, and blastn in  
the second?

Where does BLAST expect the BLOSUM62 file to be?

--
http://elfdata.com/plugin/




From pculpep at hotmail.com  Thu Feb 16 16:53:36 2006
From: pculpep at hotmail.com (Pamela Culpepper)
Date: Thu, 16 Feb 2006 21:53:36 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
In-Reply-To: <1F3D43D3-4C57-4145-B255-DF12A579A4A7@elfdata.com>
Message-ID: <BAY116-F27CD4C998063E1BE9D3CC3A0FB0@phx.gbl>

The is an environment variable -- BLASTMAT  -- that you can set to the 
location of your matrix file.
Otherwise, the data/ directory should contain the filters.

Pam

>From: "Theodore H. Smith" <delete at elfdata.com>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
>Date: Thu, 16 Feb 2006 21:43:10 +0000
>
>Hi people,
>
>I've installed blast on my computer. I'm getting some errors using a  
>custom DB.
>
>ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>ShatterProof% blastall -p blastp -d customgene.txt -i query.txt -o  
>result.out
>
>[NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>[NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill  returned 
>non-zero status
>[NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>
>
>however, this example copied from ncbi's website, works just fine:
>
>ShatterProof% cd /usr/blast/dbs/
>ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>
>I get a text file containing the result.
>
>Is that because I'm using blastp in the first attempt, and blastn in  the 
>second?
>
>Where does BLAST expect the BLOSUM62 file to be?
>
>--
>http://elfdata.com/plugin/
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From christoph.gille at charite.de  Thu Feb 16 17:03:16 2006
From: christoph.gille at charite.de (Dr. Christoph Gille)
Date: Thu, 16 Feb 2006 23:03:16 +0100 (CET)
Subject: [BiO BB] Testing blast, getting 'Unable to open BLOSUM62' error?
In-Reply-To: <1F3D43D3-4C57-4145-B255-DF12A579A4A7@elfdata.com>
References: <1F3D43D3-4C57-4145-B255-DF12A579A4A7@elfdata.com>
Message-ID: <63839.84.190.18.69.1140127396.squirrel@webmail.charite.de>

I had similiar problems some time ago and I could only blast
when I had been in the directory where blast was installed.
Even though I set all shell variables correctly.

If you do not solve this problem think about installing WU-blast
instead of NCBI. It might also be  faster.





From bioinfosm at gmail.com  Thu Feb 16 17:17:19 2006
From: bioinfosm at gmail.com (Samantha Fox)
Date: Thu, 16 Feb 2006 17:17:19 -0500
Subject: [BiO BB] BLAST problem - .index files
Message-ID: <726450810602161417l4bc339eblbd62d8e4902b61c5@mail.gmail.com>

Hi !
I got this wierd observation.. not really a problem or error, as BLAST runs
fine and gives me the output .. but something to know about.

So I format the nucleotide database as normal 'formatdb -i data -p F -o T'
.. and this makes all the relevant files.

However, I noticed that after some BLAST runs, a .index file and .index.___
also appear !! and the next BLAST runs give this sort of exception:

------------- EXCEPTION  -------------
MSG: Can't open cache file data.index: Invalid argument
STACK Bio::DB::Fasta::_open_index
/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/Fasta.pm:502
STACK Bio::DB::Fasta::index_file
/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/Fasta.pm:607
STACK Bio::DB::Fasta::new
/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/Fasta.pm:467
STACK toplevel get_ortho.pl.all:43


Any BLAST experts here, who can help !

thanks ..
~S
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From pculpep at hotmail.com  Thu Feb 16 17:30:19 2006
From: pculpep at hotmail.com (Pamela Culpepper)
Date: Thu, 16 Feb 2006 22:30:19 +0000
Subject: [BiO BB] Testing blast, getting 'Unable to open BLOSUM62' error?
In-Reply-To: <63839.84.190.18.69.1140127396.squirrel@webmail.charite.de>
Message-ID: <BAY116-F383E98B50992616898E22AA0FB0@phx.gbl>

Create a file -- .ncbirc in your home directory and add the following lines 
--

[NCBI]
data=/home/user/blast/data

[BLAST]
BLASTDB=/home/user/blast/db
BLASTMAT=/home/user/blast/data

Pam


>From: "Dr. Christoph Gille" <christoph.gille at charite.de>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Testing blast, getting 'Unable to open BLOSUM62' 
>error?
>Date: Thu, 16 Feb 2006 23:03:16 +0100 (CET)
>
>I had similiar problems some time ago and I could only blast
>when I had been in the directory where blast was installed.
>Even though I set all shell variables correctly.
>
>If you do not solve this problem think about installing WU-blast
>instead of NCBI. It might also be  faster.
>
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From delete at elfdata.com  Thu Feb 16 20:34:51 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Fri, 17 Feb 2006 01:34:51 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
In-Reply-To: <BAY116-F27CD4C998063E1BE9D3CC3A0FB0@phx.gbl>
References: <BAY116-F27CD4C998063E1BE9D3CC3A0FB0@phx.gbl>
Message-ID: <EF8E00CF-4814-46A3-8A77-B04548BA95C3@elfdata.com>

Hi Pamela,

copying my files in the data/ directory to the directory that my  
custom database is in, did work.

However, your suggestion to use the .ncbirc file made no changes, I  
was unable to get that working. This is what I put in my file:

[NCBI]
Data="/usr/blast/data"

[BLAST]
BLASTDB="/usr/blast/dbs"
BLASTMAT="/usr/blast/data"

Removing the quotes made no change.

My blast executables and folders, exist in /usr/blast/ so I have /usr/ 
blast/blastall as an executable, and /usr/blast/data as a folder  
containing BLOSUM files and the rest of the usual blast data.

What now? I'd rather be able to blast into a DB in any directory, if  
possible. Especially with custom DB's, because I'm likely to delete  
them as they are computer generated experimental DB's.

Or should I always put my custom DBs in my "/usr/blast/dbs" folder  
and be done with it?



On 16 Feb 2006, at 21:53, Pamela Culpepper wrote:

> The is an environment variable -- BLASTMAT  -- that you can set to  
> the location of your matrix file.
> Otherwise, the data/ directory should contain the filters.
>
> Pam
>
>> From: "Theodore H. Smith" <delete at elfdata.com>
>> Reply-To: "The general forum at Bioinformatics.Org"  
>> <bio_bulletin_board at bioinformatics.org>
>> To: "The general forum at Bioinformatics.Org"  
>> <bio_bulletin_board at bioinformatics.org>
>> Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62"  
>> error?
>> Date: Thu, 16 Feb 2006 21:43:10 +0000
>>
>> Hi people,
>>
>> I've installed blast on my computer. I'm getting some errors using  
>> a  custom DB.
>>
>> ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>> ShatterProof% blastall -p blastp -d customgene.txt -i query.txt - 
>> o  result.out
>>
>> [NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>> [NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill   
>> returned non-zero status
>> [NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>>
>>
>> however, this example copied from ncbi's website, works just fine:
>>
>> ShatterProof% cd /usr/blast/dbs/
>> ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>>
>> I get a text file containing the result.
>>
>> Is that because I'm using blastp in the first attempt, and blastn  
>> in  the second?
>>
>> Where does BLAST expect the BLOSUM62 file to be?




From delete at elfdata.com  Thu Feb 16 20:41:12 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Fri, 17 Feb 2006 01:41:12 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
In-Reply-To: <BAY116-F27CD4C998063E1BE9D3CC3A0FB0@phx.gbl>
References: <BAY116-F27CD4C998063E1BE9D3CC3A0FB0@phx.gbl>
Message-ID: <08688232-3FB2-4842-AB0D-573E5315BF24@elfdata.com>

Oh wait, BLASTMAT is a proper environment variable, right?

So I just need to set those lines into my unix thingy that contains  
the environment variables? I'll do that. I can figure it out myself :)

I thought blast itself actually read .ncbirc.

On 16 Feb 2006, at 21:53, Pamela Culpepper wrote:

> The is an environment variable -- BLASTMAT  -- that you can set to  
> the location of your matrix file.
> Otherwise, the data/ directory should contain the filters.
>
> Pam
>
>> From: "Theodore H. Smith" <delete at elfdata.com>
>> Reply-To: "The general forum at Bioinformatics.Org"  
>> <bio_bulletin_board at bioinformatics.org>
>> To: "The general forum at Bioinformatics.Org"  
>> <bio_bulletin_board at bioinformatics.org>
>> Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62"  
>> error?
>> Date: Thu, 16 Feb 2006 21:43:10 +0000
>>
>> Hi people,
>>
>> I've installed blast on my computer. I'm getting some errors using  
>> a  custom DB.
>>
>> ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>> ShatterProof% blastall -p blastp -d customgene.txt -i query.txt - 
>> o  result.out
>>
>> [NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>> [NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill   
>> returned non-zero status
>> [NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>>
>>
>> however, this example copied from ncbi's website, works just fine:
>>
>> ShatterProof% cd /usr/blast/dbs/
>> ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>>
>> I get a text file containing the result.
>>
>> Is that because I'm using blastp in the first attempt, and blastn  
>> in  the second?
>>
>> Where does BLAST expect the BLOSUM62 file to be?
>>
>> --
>> http://elfdata.com/plugin/
>>
>>
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>

--
http://elfdata.com/plugin/





From cmsb06 at msr-unitn.unitn.it  Fri Feb 17 04:22:14 2006
From: cmsb06 at msr-unitn.unitn.it (COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY)
Date: Fri, 17 Feb 2006 10:22:14 +0100
Subject: [BiO BB] Call for Papers CMSB06
Message-ID: <005201c633a3$a4836c40$66e8a8c0@cosbi.local>

***** Apologize for multiple copies ******

 

INTERNATIONAL CONFERENCE ON

COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY

 

18 and 19 October 2006

The Microsoft Research - University of Trento

Centre for Computational and Systems Biology

TRENTO - ITALY

http://www.msr-unitn.unitn.it/events/cmsb06.php

 

The CMSB (Computational Methods in Systems Biology) conference series was
established in 2003 to help catalyze the convergence of modellers,
physicists, mathematicians, and theoretical computer scientists from fields
such as language design, concurrency theory, program verification, and
molecular biologists, physicians, neuroscientists interested in a
systems-level understanding of cellular physiology and pathology.

 

CMSB'06 solicits original research articles (including significant
works-in-progress), surveys of current research and posters. These may cover
theoretical or applied contributions that are motivated by a biological
question and can demonstrate either actual or potential usefulness towards
answering that question. They may also cover models of computation inspired
by biological processes; the motivation may be as much computational as
biological. Particularly relevant case studies and open issues from the
biological side that demands modeling of systems are of interest as well.
The introduction of formal models should be supported by theoretical
arguments about the model and/or on the analyses that they enable, by
comparisons with other network models, and/or by examples of representation
and analysis of a biological system.

 

Topics of interest include:

1.  Biological systems and networks: inference, properties, modeling,
dynamics, simulation and reverse engineering

2.  Formal methods for drug discovery and design

3.  Methods to predict biological network behavior from incomplete
information

4.  Models including symbolic evolution and learning

5.  Models of Self-assembly

6.  Detailed case-studies on how a biological question was successfully
addressed using formal models

7.  Emergence of properties in complex biological systems

8.  Theoretical comparisons between different formal models of cellular
processes

9.  Differential, discrete and/or stochastic modeling-language frameworks

10. Quantitative formal languages

11. Biologically-inspired extensions to concurrency theory, constraint
programming, logical methods or language equivalences

12. Computer models in nano-sciences applied to biological domains

13. Definition and study of theoretical properties of biologically-inspired
formal languages

14. Biological data bases and exchange formats for biological data and
standards

 

 History

2003 held in Trento, chaired by Corrado Priami

2004 held in Paris, co-chaired by Vincent Danos and Vincent Schachter

2005 held in Edinburgh, chaired by Gordon Plotkin.

 

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Program Committee Chair

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From delete at elfdata.com  Fri Feb 17 09:45:11 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Fri, 17 Feb 2006 14:45:11 +0000
Subject: [BiO BB] Want to test a custom scoring matrix
Message-ID: <D5DFB6EE-3CB9-409D-BFA9-D7ACCE601B5E@elfdata.com>

Hi people,

I'm just playing around with BLAST to see what it outputs. I figured  
I'd better understand BLAST now as I'm going to have to understand it  
by the end of this project anyhow. (I'm at the beginning of this  
project).

I'm trying to test a made up scoring matrix. It's a very simple one.

#  Here is a matrix I made up.
    A  R  N  D  ...
A  1 -1 -1 -1
R -1  1 -1 -1
N -1 -1  1 -1
D -1 -1 -1  1
...

This is just to get a better idea of how does BLAST work. However, I  
can't figure out how to tell blast to use this matrix file! I don't  
see it in the documentation, although I might have missed something.

Any ideas anyone?

What this experiment is trying to figure out, is does BLAST return  
multiple sections, when doing local alignments. Basically, the same  
quesiton I have before about Smith-Waterman, I was trying to figure  
out how does BLAST work in the same respect. In other words, does  
BLAST match BBBBAAAA to AAAABBBB, to give the alignments:

AAAA
::::
AAAA

and

BBBB
::::
BBBB

I thought I'd figure out the answer myself instead of asking, but I  
couldn't figure out how to input custom scoring matrixes :)

--
http://elfdata.com/plugin/





From pculpep at hotmail.com  Fri Feb 17 12:29:56 2006
From: pculpep at hotmail.com (Pamela Culpepper)
Date: Fri, 17 Feb 2006 17:29:56 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
In-Reply-To: <EF8E00CF-4814-46A3-8A77-B04548BA95C3@elfdata.com>
Message-ID: <BAY116-F1B0D8059546738A829240A0F80@phx.gbl>

If you are using pre-compiled BLAST (downloaded from NCBI),  if may be 
stopping you from reading the .ncbirc file.  They have a define -- 
NCBI_DONT_USE_LOCAL_CONFIG that could be set to TRUE and that's causing the 
problem.

My .ncbirc file is --

[pac at pam-nb ~]$ more .ncbirc
[NCBI]
data=/home/pac/blast/data

[BLAST]
BLASTDB=/home/pac/blast/db
BLASTMAT=/home/pac/blast/data

and it works fine.

Go to -- http://www.lifeformulae.com/local_blast_graphics/index.html
to see how to compile BLAST for a local machine running Linux.

Pam


However, I have compiled blastall (the blast programs wrapper) from scratch.






>From: "Theodore H. Smith" <delete at elfdata.com>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" 
>error?
>Date: Fri, 17 Feb 2006 01:34:51 +0000
>
>Hi Pamela,
>
>copying my files in the data/ directory to the directory that my  custom 
>database is in, did work.
>
>However, your suggestion to use the .ncbirc file made no changes, I  was 
>unable to get that working. This is what I put in my file:
>
>[NCBI]
>Data="/usr/blast/data"
>
>[BLAST]
>BLASTDB="/usr/blast/dbs"
>BLASTMAT="/usr/blast/data"
>
>Removing the quotes made no change.
>
>My blast executables and folders, exist in /usr/blast/ so I have /usr/ 
>blast/blastall as an executable, and /usr/blast/data as a folder  
>containing BLOSUM files and the rest of the usual blast data.
>
>What now? I'd rather be able to blast into a DB in any directory, if  
>possible. Especially with custom DB's, because I'm likely to delete  them 
>as they are computer generated experimental DB's.
>
>Or should I always put my custom DBs in my "/usr/blast/dbs" folder  and be 
>done with it?
>
>
>
>On 16 Feb 2006, at 21:53, Pamela Culpepper wrote:
>
>>The is an environment variable -- BLASTMAT  -- that you can set to  the 
>>location of your matrix file.
>>Otherwise, the data/ directory should contain the filters.
>>
>>Pam
>>
>>>From: "Theodore H. Smith" <delete at elfdata.com>
>>>Reply-To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62"  
>>>error?
>>>Date: Thu, 16 Feb 2006 21:43:10 +0000
>>>
>>>Hi people,
>>>
>>>I've installed blast on my computer. I'm getting some errors using  a  
>>>custom DB.
>>>
>>>ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>>>ShatterProof% blastall -p blastp -d customgene.txt -i query.txt - o  
>>>result.out
>>>
>>>[NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>>>[NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill   
>>>returned non-zero status
>>>[NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>>>
>>>
>>>however, this example copied from ncbi's website, works just fine:
>>>
>>>ShatterProof% cd /usr/blast/dbs/
>>>ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>>>
>>>I get a text file containing the result.
>>>
>>>Is that because I'm using blastp in the first attempt, and blastn  in  
>>>the second?
>>>
>>>Where does BLAST expect the BLOSUM62 file to be?
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From marty.gollery at gmail.com  Fri Feb 17 13:18:27 2006
From: marty.gollery at gmail.com (Martin Gollery)
Date: Fri, 17 Feb 2006 10:18:27 -0800
Subject: [BiO BB] Want to test a custom scoring matrix
In-Reply-To: <D5DFB6EE-3CB9-409D-BFA9-D7ACCE601B5E@elfdata.com>
References: <D5DFB6EE-3CB9-409D-BFA9-D7ACCE601B5E@elfdata.com>
Message-ID: <bdd10c2a0602171018l628d7042oa08d9364c00ad12e@mail.gmail.com>

Hi Theodore,

For serious work, I don't recommend this, because you would really have to
recalculate lamba and the gap penalties. For playing around, you can specify
the matrix with -M. The easiest thing to do is to backup BLOSUM62, then save
your test matrix with that name. Sneaky, but I think it will work.

Marty

On 2/17/06, Theodore H. Smith <delete at elfdata.com> wrote:
>
> Hi people,
>
> I'm just playing around with BLAST to see what it outputs. I figured
> I'd better understand BLAST now as I'm going to have to understand it
> by the end of this project anyhow. (I'm at the beginning of this
> project).
>
> I'm trying to test a made up scoring matrix. It's a very simple one.
>
> #  Here is a matrix I made up.
>     A  R  N  D  ...
> A  1 -1 -1 -1
> R -1  1 -1 -1
> N -1 -1  1 -1
> D -1 -1 -1  1
> ...
>
> This is just to get a better idea of how does BLAST work. However, I
> can't figure out how to tell blast to use this matrix file! I don't
> see it in the documentation, although I might have missed something.
>
> Any ideas anyone?
>
> What this experiment is trying to figure out, is does BLAST return
> multiple sections, when doing local alignments. Basically, the same
> quesiton I have before about Smith-Waterman, I was trying to figure
> out how does BLAST work in the same respect. In other words, does
> BLAST match BBBBAAAA to AAAABBBB, to give the alignments:
>
> AAAA
> ::::
> AAAA
>
> and
>
> BBBB
> ::::
> BBBB
>
> I thought I'd figure out the answer myself instead of asking, but I
> couldn't figure out how to input custom scoring matrixes :)
>
> --
> http://elfdata.com/plugin/
>
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>



--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-----------
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From pculpep at hotmail.com  Sat Feb 18 12:26:46 2006
From: pculpep at hotmail.com (Pamela Culpepper)
Date: Sat, 18 Feb 2006 17:26:46 +0000
Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?
In-Reply-To: <08688232-3FB2-4842-AB0D-573E5315BF24@elfdata.com>
Message-ID: <BAY116-F249F851B09E1296744DB9DA0F90@phx.gbl>

right.


>From: "Theodore H. Smith" <delete at elfdata.com>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" 
>error?
>Date: Fri, 17 Feb 2006 01:41:12 +0000
>
>Oh wait, BLASTMAT is a proper environment variable, right?
>
>So I just need to set those lines into my unix thingy that contains  the 
>environment variables? I'll do that. I can figure it out myself :)
>
>I thought blast itself actually read .ncbirc.
>
>On 16 Feb 2006, at 21:53, Pamela Culpepper wrote:
>
>>The is an environment variable -- BLASTMAT  -- that you can set to  the 
>>location of your matrix file.
>>Otherwise, the data/ directory should contain the filters.
>>
>>Pam
>>
>>>From: "Theodore H. Smith" <delete at elfdata.com>
>>>Reply-To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62"  
>>>error?
>>>Date: Thu, 16 Feb 2006 21:43:10 +0000
>>>
>>>Hi people,
>>>
>>>I've installed blast on my computer. I'm getting some errors using  a  
>>>custom DB.
>>>
>>>ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>>>ShatterProof% blastall -p blastp -d customgene.txt -i query.txt - o  
>>>result.out
>>>
>>>[NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>>>[NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill   
>>>returned non-zero status
>>>[NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>>>
>>>
>>>however, this example copied from ncbi's website, works just fine:
>>>
>>>ShatterProof% cd /usr/blast/dbs/
>>>ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>>>
>>>I get a text file containing the result.
>>>
>>>Is that because I'm using blastp in the first attempt, and blastn  in  
>>>the second?
>>>
>>>Where does BLAST expect the BLOSUM62 file to be?
>>>
>>>--
>>>http://elfdata.com/plugin/
>>>
>>>
>>>_______________________________________________
>>>Bioinformatics.Org general forum  -   
>>>BiO_Bulletin_Board at bioinformatics.org
>>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>>_______________________________________________
>>Bioinformatics.Org general forum  -   
>>BiO_Bulletin_Board at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>
>--
>http://elfdata.com/plugin/
>
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From ahmed at pobox.com  Fri Feb 17 19:59:52 2006
From: ahmed at pobox.com (Ahmed Moustafa)
Date: Fri, 17 Feb 2006 18:59:52 -0600
Subject: [BiO BB] phylogeny search engine?
Message-ID: <43F67188.6010700@pobox.com>

Hi All!


We are working on a project where we need to search a large number of 
phylogeny trees for an approximate (or exact) containment of a query 
tree, what tool/algorithm would help achieving that?

Your help will be appreciated so much!

Ahmed



From dmb at mrc-dunn.cam.ac.uk  Sun Feb 19 08:36:42 2006
From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser)
Date: Sun, 19 Feb 2006 13:36:42 +0000
Subject: [BiO BB] phylogeny search engine?
In-Reply-To: <43F67188.6010700@pobox.com>
References: <43F67188.6010700@pobox.com>
Message-ID: <43F8746A.5080203@mrc-dunn.cam.ac.uk>

Ahmed Moustafa wrote:
> Hi All!
> 
> 
> We are working on a project where we need to search a large number of 
> phylogeny trees for an approximate (or exact) containment of a query 
> tree, what tool/algorithm would help achieving that?
> 
> Your help will be appreciated so much!
> 

You should be able to do 'sub tree matching' quite easily, but 'ontology 
alignment' is a big research field! So far as I know there are no 'exact 
algorithms' for 'approximate sub tree matching'.

> Ahmed
> 
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From maximilianh at gmail.com  Sun Feb 19 08:52:37 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Sun, 19 Feb 2006 14:52:37 +0100
Subject: [BiO BB] Tool to mutate DNA sequence
In-Reply-To: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
Message-ID: <76f031ae0602190552v5f2542dbv@mail.gmail.com>

Hi bio-mailinglists,

does anyone here know of a tool or a library to display two (or more)
sequences at the same time with coloured features? Possibly with lines,
connecting some features from one sequence to the other (synteny-plot) ?
Or to display two multiple alignments, one on top of each other, with
colored features added?

It's not that it would be difficult to write, but programming visualisation
usually takes a lot of time.
Bio::Graphics seems mainly concerned with one main sequence and features on
it. Well, I could copy together two of these gif-images, but then there
would be no connecting lines. Same applies for the graphics in Biojava or
the gff2ps tool or all the multiple alignment viewers that I know (Bioedit,
ClustalX). There is something called Toucan in Java, which displays at least
several lines of gff-style-features, but no visible sequences and more
importantly, no connecting lines. A recent software, Djinn lite, is using a
similar kind of visualization to compare different spliced genes from
various species, but it's mainly aimed at splicing and written in Visual
Basic.
I guess a good compromise might be the 3D viewer Sockeye, but I haven't seen
any synteny-lines in sockeye yet.

I guess I must have missed something here. I cannot be the first one that
would like to compare, say, two gff files, or two multiple alignments?

Thanks a lot for any idea,
Max
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From bikram80 at gmail.com  Sun Feb 19 09:06:02 2006
From: bikram80 at gmail.com (Bikram Nayak)
Date: Sun, 19 Feb 2006 19:36:02 +0530
Subject: [BiO BB] Tool to mutate DNA sequence
In-Reply-To: <76f031ae0602190552v5f2542dbv@mail.gmail.com>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<76f031ae0602190552v5f2542dbv@mail.gmail.com>
Message-ID: <16f934830602190606x1e8c5b42k42c1b74da903ce8d@mail.gmail.com>

yes i know but why i would tell u ? import  tcl tk package from CPAN
,naughty
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From moyc at mail.med.upenn.edu  Sun Feb 19 13:51:15 2006
From: moyc at mail.med.upenn.edu (Christopher Moy)
Date: Sun, 19 Feb 2006 13:51:15 -0500
Subject: [BiO BB] Gene Search in Worm
Message-ID: <20fdce30fd904ecbe4dad8f3196c463c@mail.med.upenn.edu>

Hello,

I have been trying to find a gene in worm that has orthologs in higher 
order taxa (human, chimp, dog, etc) and in fungi (yeast, candid 
albicans, etc). Using the protein database from wormbase I have ran 
HMM, PSI-BLAST, FuzzPro, MEME and BLOCKS to find a similar domain 
structure shared among all homologs. Although I find some loose 
e-values (.001-.1) but the proteins that have this score fail to 
contain distinct domains that is shared among all putative orthologs. 
 From what I can tell, it is possible that there are no proteins in the 
current wormpep database. I have also performed tblastn runs using 
various orthologs as queries to search for genome wide hits to the worm 
but any prospective ortholog fails to contain the domains in other 
orthologs. Does anyone have any other suggestions for further 
searching? Should I consider a more comprehensive sequence alignment 
strategy (Smith Waterman,etc).

Note: There is no putative structure for this gene available right now.

Chris



From hararid at bgumail.bgu.ac.il  Sun Feb 19 14:11:11 2006
From: hararid at bgumail.bgu.ac.il (hararid at bgumail.bgu.ac.il)
Date: Sun, 19 Feb 2006 21:11:11 +0200
Subject: [BiO BB] Gene Search in Worm
Message-ID: <20060219190053.27B1A33E78@smtp2.bgu.ac.il>

Chris,

It is possible that your worm gene does not have homologues in higher organisms, although it is likely that you will find homologs amongst different worm species.  Many such examples exist.  The same goes for flies, etc.

The most sensitive search that you can perform in which to hunt for homologs is to perform the following:  Extract the homologs from different worm species.  Create a multiple sequence alignment (E.g. ClustalW).  Then use the multiple sequence alignment to generate a PROFILE.   You can then run this profile againt various databases (IE: profilesearches).  This can be done using the HMMER algorithm or using a Smith-Waterman based profilesearch algorithm. For the latter I refer you to this site:
http://eta.embl-heidelberg.de:8000/misc/

Daniel

hararid at bgu.ac.il


> 
> From: Christopher Moy <moyc at mail.med.upenn.edu>
> Date: 2006/02/19 ? PM 08:51:15 GMT+02:00
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] Gene Search in Worm
> 
> Hello,
> 
> I have been trying to find a gene in worm that has orthologs in higher 
> order taxa (human, chimp, dog, etc) and in fungi (yeast, candid 
> albicans, etc). Using the protein database from wormbase I have ran 
> HMM, PSI-BLAST, FuzzPro, MEME and BLOCKS to find a similar domain 
> structure shared among all homologs. Although I find some loose 
> e-values (.001-.1) but the proteins that have this score fail to 
> contain distinct domains that is shared among all putative orthologs. 
>  From what I can tell, it is possible that there are no proteins in the 
> current wormpep database. I have also performed tblastn runs using 
> various orthologs as queries to search for genome wide hits to the worm 
> but any prospective ortholog fails to contain the domains in other 
> orthologs. Does anyone have any other suggestions for further 
> searching? Should I consider a more comprehensive sequence alignment 
> strategy (Smith Waterman,etc).
> 
> Note: There is no putative structure for this gene available right now.
> 
> Chris
> 
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 



From delete at elfdata.com  Sun Feb 19 16:54:53 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Sun, 19 Feb 2006 21:54:53 +0000
Subject: [BiO BB] More Smith-Waterman internals. Gaps extensions this time.
Message-ID: <16071B28-7A8E-4E30-A3D9-1A4DC1A6B46D@elfdata.com>


Hi people,

Is there anyone out there with enough knowledge of the arcane field  
of Smith-Waterman matrixes to answer this?

OK, so Smith-Waterman is best done using a gap penalty that can has a  
start cost, and an extension cost.

I want to implement a Smith-Waterman algorithm.

Must I maintain a "gap or not" matrix alongside the cell score matrix?

I'd rather not if it were possible and not wasting CPU time. Because  
maintaining and processing two matrixes, effectively makes my  
algorithm run at 2x as slow as it would otherwise!

If there is a nice simple trick to avoid needing two matrixes, that  
would be great. If not, well at least I know.

The answer could really be something obvious like "well I can't see  
any way to avoid needing two matrixes, it looks pretty much like  
you'll have to use two" :)

Maybe someone better than me with this stuff has a good answer.

--
http://elfdata.com/plugin/





From idoerg at burnham.org  Sun Feb 19 22:34:12 2006
From: idoerg at burnham.org (Iddo Friedberg)
Date: Sun, 19 Feb 2006 19:34:12 -0800
Subject: [BiO BB] More Smith-Waterman internals. Gaps extensions this time.
In-Reply-To: <16071B28-7A8E-4E30-A3D9-1A4DC1A6B46D@elfdata.com>
Message-ID: <Pine.SGI.4.10.10602191923340.1907514-100000@pines2.ljcrf.edu>




On Sun, 19 Feb 2006, Theodore H. Smith wrote:

> 
> Hi people,
> 
> Is there anyone out there with enough knowledge of the arcane field  
> of Smith-Waterman matrixes to answer this?
> 
> OK, so Smith-Waterman is best done using a gap penalty that can has a  
> start cost, and an extension cost.
> 
> I want to implement a Smith-Waterman algorithm.
> 
> Must I maintain a "gap or not" matrix alongside the cell score matrix?
> 

If I understand your question correctly, it seems like you should pick
up a good Bioinformatics textbook and / or read the original Smith
Waterman paper. I'm not sure how exactly you want to implemement SW given
your question.

The short answer is "no". When building the distance matrix, you use the
gap insertion and extension penalties as initially given to generate the
values of that matrix.

Here is a free resource explaining the basics of dynamic programming for
sequence alignment, of which SW is a variant.

http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/prwali.html

HTH,

Iddo


--
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://iddo-friedberg.org
http://BioFunctionPrediction.org





From shameer at ncbs.res.in  Mon Feb 20 01:21:01 2006
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Mon, 20 Feb 2006 11:51:01 +0530 (IST)
Subject: [BiO BB] Matrix Average Code / Module ? 
In-Reply-To: <76f031ae0602190552v5f2542dbv@mail.gmail.com>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<76f031ae0602190552v5f2542dbv@mail.gmail.com>
Message-ID: <59825.192.168.1.176.1140416461.squirrel@192.168.1.176>

Hi all,
Is there any program/module to calculate the average of a blosum/pam any
matrix ?

I have a matrix and I need to see the average

for example

11 22 43 54 50
27 87 74 32 10
66 58 98 78 20
22 23 44 16 34

I have gone through Bio::Matrix::MatrixI and Bio::Matrix::GenericMatrix
and other perl modules like Math::Matrix
http://search.cpan.org/~ulpfr/Math-Matrix-0.4/Matrix.pm
and Math::Cephes::Matrix - but none of them have a provison to do matrix 
average calculation.

Any help ???
thanks in advance,
Happy biocomputing !!!


-- 
Shameer Khadar
National Centre for Biological Sciences (TIFR)
UAS - GKVK Campus - Bellary Road Bangalore - 65 - Karnataka - India
T - 91-080-23636420-32 EXT 4241
F - 91-080-23636662/23636675
W - http://www.ncbs.res.in
--------------------------------------------------
"Refrain from illusions, insist on work and not words,
 patiently seek divine and scientific truth."
MM




From gbottu at ben.vub.ac.be  Mon Feb 20 03:04:11 2006
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Mon, 20 Feb 2006 09:04:11 +0100
Subject: [EMBOSS] [BiO BB] Tool to mutate DNA sequence - Checked by
	AntiVir 
In-Reply-To: <76f031ae0602190552v5f2542dbv@mail.gmail.com>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<76f031ae0602190552v5f2542dbv@mail.gmail.com>
Message-ID: <20060220080411.GB26540@bigben.ulb.ac.be>

On Sun, Feb 19, 2006 at 02:52:37PM +0100, Maximilian Haeussler wrote:
> does anyone here know of a tool or a library to display two (or more)
> sequences at the same time with coloured features? Possibly with lines,
> connecting some features from one sequence to the other (synteny-plot) ?
> Or to display two multiple alignments, one on top of each other, with
> colored features added?

Well, there is Alfresco
http://www.sanger.ac.uk/Software/Alfresco/

	Guy Bottu,
	Belgian EMBnet Node



From khoueiry at ibdm.univ-mrs.fr  Mon Feb 20 04:27:07 2006
From: khoueiry at ibdm.univ-mrs.fr (khoueiry)
Date: Mon, 20 Feb 2006 10:27:07 +0100
Subject: [Bioperl-l] [BiO BB] Tool to mutate DNA sequence
In-Reply-To: <76f031ae0602190552v5f2542dbv@mail.gmail.com>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<76f031ae0602190552v5f2542dbv@mail.gmail.com>
Message-ID: <1140427628.10569.10.camel@localhost>

Hi Maximilian,

    I hope that I understand your question. An easy way to do so is to
put your sequences in a separate arrays, loop overs these arrays while
comparing positions, if the nuc/aa are equal, then push a pipe  ( "|" )
in a third separate array, else push a space ( " " ). Once it's done,
print your arrays by looping over them...


array1 qw (A A G C T)
array2 qw (C A C C G)
array3 qw (  |   |  )

Then, print your arrays and that will give you

A A G C T
  |   | 
C A C C G

Surely, you can color whatever you want in that case too (i.e : the aligned nuc).



Hope this was clear

Pierre



On Sun, 2006-02-19 at 14:52 +0100, Maximilian Haeussler wrote:

> Hi bio-mailinglists,
> 
> does anyone here know of a tool or a library to display two (or more)
> sequences at the same time with coloured features? Possibly with lines,
> connecting some features from one sequence to the other (synteny-plot) ?
> Or to display two multiple alignments, one on top of each other, with
> colored features added?
> 
> It's not that it would be difficult to write, but programming visualisation
> usually takes a lot of time.
> Bio::Graphics seems mainly concerned with one main sequence and features on
> it. Well, I could copy together two of these gif-images, but then there
> would be no connecting lines. Same applies for the graphics in Biojava or
> the gff2ps tool or all the multiple alignment viewers that I know (Bioedit,
> ClustalX). There is something called Toucan in Java, which displays at least
> several lines of gff-style-features, but no visible sequences and more
> importantly, no connecting lines. A recent software, Djinn lite, is using a
> similar kind of visualization to compare different spliced genes from
> various species, but it's mainly aimed at splicing and written in Visual
> Basic.
> I guess a good compromise might be the 3D viewer Sockeye, but I haven't seen
> any synteny-lines in sockeye yet.
> 
> I guess I must have missed something here. I cannot be the first one that
> would like to compare, say, two gff files, or two multiple alignments?
> 
> Thanks a lot for any idea,
> Max
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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From ahmed at users.sourceforge.net  Mon Feb 20 12:28:28 2006
From: ahmed at users.sourceforge.net (Ahmed Moustafa)
Date: Mon, 20 Feb 2006 11:28:28 -0600
Subject: [BiO BB] phylogeny search engine?
In-Reply-To: <43F8746A.5080203@mrc-dunn.cam.ac.uk>
References: <43F67188.6010700@pobox.com> <43F8746A.5080203@mrc-dunn.cam.ac.uk>
Message-ID: <43F9FC3C.10404@users.sourceforge.net>

Hi Dan,

Could you please give more details on how do "sub tree matching" (e.g. 
which algorithm)?

Thanks,

Ahmed

On 2/19/2006 7:36 AM, Dan Bolser wrote:

> Ahmed Moustafa wrote:
>
>> Hi All!
>>
>>
>> We are working on a project where we need to search a large number of 
>> phylogeny trees for an approximate (or exact) containment of a query 
>> tree, what tool/algorithm would help achieving that?
>>
>> Your help will be appreciated so much!
>>
>
> You should be able to do 'sub tree matching' quite easily, but 
> 'ontology alignment' is a big research field! So far as I know there 
> are no 'exact algorithms' for 'approximate sub tree matching'.



From boris.steipe at utoronto.ca  Mon Feb 20 13:40:19 2006
From: boris.steipe at utoronto.ca (Boris Steipe)
Date: Mon, 20 Feb 2006 13:40:19 -0500
Subject: [BiO BB] Re: [Bioperl-l] Matrix Average Code / Module ?
In-Reply-To: <59825.192.168.1.176.1140416461.squirrel@192.168.1.176>
References: <003b01c62d33$d37d15d0$e6028a0a@GOLHARMOBILE1>
	<76f031ae0602190552v5f2542dbv@mail.gmail.com>
	<59825.192.168.1.176.1140416461.squirrel@192.168.1.176>
Message-ID: <92CF0104-0524-4BA3-B039-3CEECF68E20B@utoronto.ca>

Assuming you mean the arithmetic average of all elements in a matrix,  
you could do the following (using your numbers):


#!/usr/bin/perl -w
use strict;

my @matrix;

push(@matrix, [(11,22,43,54,50)]); # [(...)] :a list passed as an  
anonymous array
push(@matrix, [(27,87,74,32,10)]);
push(@matrix, [(66,58,98,78,20)]);
push(@matrix, [(22,23,44,16,34)]);

my $sum = 0;
my $number = 0;

foreach my $row (@matrix) {
     foreach my $element (@{$row}){
         $sum += $element;
         $number++;
     }
}

print "Average of $number elements = ", $sum/$number,"\n";
exit;


HTH,

B.




On 20 Feb 2006, at 01:21, Shameer Khadar wrote:

> Hi all,
> Is there any program/module to calculate the average of a blosum/ 
> pam any
> matrix ?
>
> I have a matrix and I need to see the average
>
> for example
>
> 11 22 43 54 50
> 27 87 74 32 10
> 66 58 98 78 20
> 22 23 44 16 34
>
> I have gone through Bio::Matrix::MatrixI and  
> Bio::Matrix::GenericMatrix
> and other perl modules like Math::Matrix
> http://search.cpan.org/~ulpfr/Math-Matrix-0.4/Matrix.pm
> and Math::Cephes::Matrix - but none of them have a provison to do  
> matrix
> average calculation.
>
> Any help ???
> thanks in advance,
> Happy biocomputing !!!
>
>
> -- 
> Shameer Khadar
> National Centre for Biological Sciences (TIFR)
> UAS - GKVK Campus - Bellary Road Bangalore - 65 - Karnataka - India
> T - 91-080-23636420-32 EXT 4241
> F - 91-080-23636662/23636675
> W - http://www.ncbs.res.in
> --------------------------------------------------
> "Refrain from illusions, insist on work and not words,
>  patiently seek divine and scientific truth."
> MM
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From smagarwal at yahoo.com  Tue Feb 21 00:03:24 2006
From: smagarwal at yahoo.com (Subhash Agarwal)
Date: Tue, 21 Feb 2006 05:03:24 +0000 (GMT)
Subject: [BiO BB] Mean and Standard deviation
Message-ID: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>

Dear Forum Memebers
   
  I have a dataset with 394 data points. The frequecy distribution of which is as follows:
   
                0-0.02  85    0.02-0.04  63    0.04-0.06  51    0.06-0.08  39    0.08-0.1  36    0.10-0.12  24    -0.12-0.14  21    0.14-0.16  19    0.16-0.18  13    0.18-0.2  10            >0.20            33
   
  The mean and SD of the data is 0.0842 and 0.0853. But when the data points from 0-0.02 and > 0.2 are removed and the mean and SD is calculated it is found that mean doesnt change much (0.0819) but SD does (0.0472). My query is what can I interpret from this regarding the data.
   
  If any of the forum members feels that this question should be addressed to some other place do let me know.
   
  Thanks
  Subhash

				
---------------------------------
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
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From siowcheng82 at yahoo.com  Tue Feb 21 04:34:42 2006
From: siowcheng82 at yahoo.com (chan cheng)
Date: Tue, 21 Feb 2006 01:34:42 -0800 (PST)
Subject: [BiO BB] how to get PSSM profile from PSI-BLAST
Message-ID: <20060221093442.93682.qmail@web34311.mail.mud.yahoo.com>

I m doing a research about prediction of beta turns in
proteins from multiple alignment using neural network.
I had paste the beta turn sequence in PSI-BLAST and
summit the form. however i cant get the PSSM profile
that I need it as my neural network input.
how can i get the profile from PSI-BLAST?

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From karen.morris at bbsrc.ac.uk  Tue Feb 21 06:45:41 2006
From: karen.morris at bbsrc.ac.uk (karen morris (RRes-Roth))
Date: Tue, 21 Feb 2006 11:45:41 -0000
Subject: [BiO BB] 3rd Integrative Bioinformatics Workshop
Message-ID: <EFDAAE7F4B83D243868A2F25AD8A4B38050626A7@rothe2ksrv1.rothamsted.bbsrc.ac.uk>

*** CALL FOR PAPERS ***

3rd Integrative Bioinformatics Workshop
September 4-6, 2006
Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
http://www.rothamsted.bbsrc.ac.uk/bab/conf/ibiof/

Accepted papers will also appear in the Journal of Integrative
Bioinformatics http://journal.imbio.de/

DESCRIPTION
Biological data are scattered across hundreds of biological databases
and thousands of scientific journals. Current high throughput genomics
technologies generate large quantities of high dimensional data.
Microarray, NMR, mass spectrometry, protein chips, gel electrophoresis
data, Yeast-Two-Hybrid, QTL mapping, gene silencing and knockout
experiments are all examples of technologies that capture thousands of
data points, often in single experiments. The challenge for Integrative
Bioinformatics is to capture, model, integrate and analyse these data in
a consistent way to provide new and deeper insights into complex
biological systems. 
This, third workshop on Integrative Bioinformatics will be of interest
to Bioinformaticians, Computer Scientists and others working in, or
interested in finding out more about, the developing area of integrative
bioinformatics. There will be opportunities to present and discuss
methods, theoretical approaches or their practical applications.  

TOPICS
Database Integration
Combined dry and wetlab studies 
Molecular Databases / Data Warehouses 
Errors and inconsistencies in biological databases 
Prediction and Integration of Metabolic and Regulatory Networks 
Genotype - phenotype linkage 
Protein-Protein-Interactions 
Microarray Modeling and Analyses 
Integrative Approaches for Drug Design 
Computational Infrastructure for Biotechnology 
Virtual Cell Modeling 
Gene Identification, Regulation and Expression 
Identification of Gene Regulatory Networks 
Computational Systems Biology 
Computational Proteomics 
Optimization of Workflow Management in Bioinformatics 
Bio Ontologies 
Quality and consistency of ontologies 
Integrative modeling and simulation frameworks 
Integrative data and text mining approaches 
 
IMPORTANT DATES
May  8: 	Paper submission deadline
June 23:	Notification of acceptance for papers
July 17:	Camera ready paper submission deadline
August 1:	Registration deadline
August 15:	Poster submission deadline


Karen Morris

Rothamsted Research
Harpenden
Herts
AL5 2JQ

Telephone Number: 01582 763133 Extension 2813


From CHRISTOPHER_FRENZ at NYMC.EDU  Tue Feb 21 11:57:39 2006
From: CHRISTOPHER_FRENZ at NYMC.EDU (Frenz, Christopher)
Date: Tue, 21 Feb 2006 11:57:39 -0500
Subject: [BiO BB] Mean and Standard deviation
References: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
Message-ID: <70C50B8807B54A429AC206E83A3BA6BCAD8C5C@mail.nymc.edu>

SD calculations involve the sample size as one of the variables.  This is likely what is causing the change in SD, since you are reducing the the sample size when you remove the two sets of endpoints.

Chris


-----Original Message-----
From: bio_bulletin_board-bounces+christopher_frenz=nymc.edu at bioinformatics.org on behalf of Subhash Agarwal
Sent: Tue 2/21/2006 12:03 AM
To: bioinformatics.org
Subject: [BiO BB] Mean and Standard deviation
 
Dear Forum Memebers
   
  I have a dataset with 394 data points. The frequecy distribution of which is as follows:
   
                0-0.02  85    0.02-0.04  63    0.04-0.06  51    0.06-0.08  39    0.08-0.1  36    0.10-0.12  24    -0.12-0.14  21    0.14-0.16  19    0.16-0.18  13    0.18-0.2  10            >0.20            33
   
  The mean and SD of the data is 0.0842 and 0.0853. But when the data points from 0-0.02 and > 0.2 are removed and the mean and SD is calculated it is found that mean doesnt change much (0.0819) but SD does (0.0472). My query is what can I interpret from this regarding the data.
   
  If any of the forum members feels that this question should be addressed to some other place do let me know.
   
  Thanks
  Subhash

				
---------------------------------
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

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From marty.gollery at gmail.com  Tue Feb 21 14:12:10 2006
From: marty.gollery at gmail.com (Martin Gollery)
Date: Tue, 21 Feb 2006 11:12:10 -0800
Subject: [BiO BB] how to get PSSM profile from PSI-BLAST
In-Reply-To: <20060221093442.93682.qmail@web34311.mail.mud.yahoo.com>
References: <20060221093442.93682.qmail@web34311.mail.mud.yahoo.com>
Message-ID: <bdd10c2a0602211112i3e9318eeh1ff0691343382cc0@mail.gmail.com>

Hi Chan,

To output the profile, use the -C option, as in
blastpgp -d nr -i myfile.faa -C myprofile.ckp -j 3

This will save the profile as myprofile.ckp.

Marty

On 2/21/06, chan cheng <siowcheng82 at yahoo.com> wrote:
>
> I m doing a research about prediction of beta turns in
> proteins from multiple alignment using neural network.
> I had paste the beta turn sequence in PSI-BLAST and
> summit the form. however i cant get the PSSM profile
> that I need it as my neural network input.
> how can i get the profile from PSI-BLAST?
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>



--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-----------
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From aloraine at gmail.com  Tue Feb 21 15:22:27 2006
From: aloraine at gmail.com (Ann Loraine)
Date: Tue, 21 Feb 2006 14:22:27 -0600
Subject: [BiO BB] collecting all genes with a given GO id or its child terms
Message-ID: <83722dde0602211222l30f0c88cye4e5aeae29d81d45@mail.gmail.com>

Hi,

Maybe somebody on the list could point me in the right direction?

I'm looking for something that takes a list of GO ids and then returns
a list of all Arabidopsis 'AGI' codes (gene ids, e.g., AT4G30490 )
that have been annotated with a GO id on the list and/or the child
term of any GO term on the list.

All the best,

Ann Loraine

--
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org


From CHRISTOPHER_FRENZ at NYMC.EDU  Tue Feb 21 12:40:37 2006
From: CHRISTOPHER_FRENZ at NYMC.EDU (Frenz, Christopher)
Date: Tue, 21 Feb 2006 12:40:37 -0500
Subject: [BiO BB] Mean and Standard deviation
References: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
Message-ID: <70C50B8807B54A429AC206E83A3BA6BCAD8C5E@mail.nymc.edu>

Oops!  Missed the fact that he posted the SD values, so I didn't note the direction of the change.  Let's give a full explanation this time.

SD= sqrt(Summation((Xi-Mean)^2)/(n-1)) where Xi is used to iterate through each value in the data set.  Basically you begin by summing the squared differences between the mean and each value in the data set.  Getting rid of the endpoints will likely lessen the value of this number resulting in a smaller SD, since the remaining numbers will result in smaller differences with the mean.  This number is then divided by (n-1), where n is the sample size.  Thus a smaller n will result in a larger SD and a larger n will result in a smaller SD.  The final value of SD is the number square root of the number that results from the division by (n-1).  

Chris




-----Original Message-----
From: bio_bulletin_board-bounces+christopher_frenz=nymc.edu at bioinformatics.org on behalf of Subhash Agarwal
Sent: Tue 2/21/2006 12:03 AM
To: bioinformatics.org
Subject: [BiO BB] Mean and Standard deviation
 
Dear Forum Memebers
   
  I have a dataset with 394 data points. The frequecy distribution of which is as follows:
   
                0-0.02  85    0.02-0.04  63    0.04-0.06  51    0.06-0.08  39    0.08-0.1  36    0.10-0.12  24    -0.12-0.14  21    0.14-0.16  19    0.16-0.18  13    0.18-0.2  10            >0.20            33
   
  The mean and SD of the data is 0.0842 and 0.0853. But when the data points from 0-0.02 and > 0.2 are removed and the mean and SD is calculated it is found that mean doesnt change much (0.0819) but SD does (0.0472). My query is what can I interpret from this regarding the data.
   
  If any of the forum members feels that this question should be addressed to some other place do let me know.
   
  Thanks
  Subhash

				
---------------------------------
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

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From marty.gollery at gmail.com  Tue Feb 21 12:17:56 2006
From: marty.gollery at gmail.com (Martin Gollery)
Date: Tue, 21 Feb 2006 09:17:56 -0800
Subject: [BiO BB] Mean and Standard deviation
In-Reply-To: <70C50B8807B54A429AC206E83A3BA6BCAD8C5C@mail.nymc.edu>
References: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
	<70C50B8807B54A429AC206E83A3BA6BCAD8C5C@mail.nymc.edu>
Message-ID: <bdd10c2a0602210917g70edb384l5d1a6328629f0a2b@mail.gmail.com>

Chris is correct. Another way to look at it is to consider that you are
removing the values that have the greatest deviation from the mean, and so
it makes sense that you then have a lower standard deviation.

Marty

On 2/21/06, Frenz, Christopher <CHRISTOPHER_FRENZ at nymc.edu> wrote:
>
> SD calculations involve the sample size as one of the variables.  This is
> likely what is causing the change in SD, since you are reducing the the
> sample size when you remove the two sets of endpoints.
>
> Chris
>
>
> -----Original Message-----
> From: bio_bulletin_board-bounces+christopher_frenz=
> nymc.edu at bioinformatics.org on behalf of Subhash Agarwal
> Sent: Tue 2/21/2006 12:03 AM
> To: bioinformatics.org
> Subject: [BiO BB] Mean and Standard deviation
>
> Dear Forum Memebers
>
>   I have a dataset with 394 data points. The frequecy distribution of
> which is as follows:
>
>                 0-0.02  85    0.02-0.04  63    0.04-0.06  51    0.06-0.08
>   39    0.08-0.1  36    0.10-0.12  24    -0.12-0.14  21    0.14-0.16
>   19    0.16-0.18  13    0.18-0.2  10            >0.20            33
>
>   The mean and SD of the data is 0.0842 and 0.0853. But when the data
> points from 0-0.02 and > 0.2 are removed and the mean and SD is calculated
> it is found that mean doesnt change much (0.0819) but SD does (0.0472). My
> query is what can I interpret from this regarding the data.
>
>   If any of the forum members feels that this question should be addressed
> to some other place do let me know.
>
>   Thanks
>   Subhash
>
>
> ---------------------------------
> Jiyo cricket on Yahoo! India cricket
> Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>


--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-----------
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From ryan.raaum at gmail.com  Tue Feb 21 12:41:22 2006
From: ryan.raaum at gmail.com (Ryan Raaum)
Date: Tue, 21 Feb 2006 12:41:22 -0500
Subject: [BiO BB] Mean and Standard deviation
In-Reply-To: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
References: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
Message-ID: <a33f26610602210941x214695a1s59d7e12c3bf6a26e@mail.gmail.com>

Hi,

One thing you might consider is that your data are nowhere near normally
distributed, so it's unclear how mean and standard deviation are useful
summary statistics for these data.

Best,

Ryan

On 2/21/06, Subhash Agarwal <smagarwal at yahoo.com> wrote:
>
> Dear Forum Memebers
>
> I have a dataset with 394 data points. The frequecy distribution of which
> is as follows:
>
>     0-0.02 85 0.02-0.04 63 0.04-0.06 51 0.06-0.08 39 0.08-0.1 36 0.10-0.12
> 24 -0.12-0.14 21 0.14-0.16 19 0.16-0.18 13 0.18-0.2 10            >0.20
>             33
>
> The mean and SD of the data is 0.0842 and 0.0853. But when the data points
> from 0-0.02 and > 0.2 are removed and the mean and SD is calculated it is
> found that mean doesnt change much (0.0819) but SD does (0.0472). My query
> is what can I interpret from this regarding the data.
>
> If any of the forum members feels that this question should be addressed
> to some other place do let me know.
>
> Thanks
> Subhash
>
> ------------------------------
> Jiyo cricket on Yahoo! India cricket<http://us.rd.yahoo.com/mail/in/mailcricket/*http://in.sports.yahoo.com/cricket/>
> Yahoo! Messenger Mobile<http://us.rd.yahoo.com/mail/in/mailmobilemessenger/*http://in.mobile.yahoo.com/new/messenger/>Stay in touch with your buddies all the time.
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>


--
Ryan Raaum
http://www.rockefeller.edu -- Bacterial Pathogenesis and Immunology
http://www.worldmartial.com -- Black Belt Instructor
http://locomotive.raaum.org -- Self contained one-click Rails for Mac OS X
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From chea at mail.nih.gov  Tue Feb 21 15:34:25 2006
From: chea at mail.nih.gov (Che, Anney (NIHNIAID))
Date: Tue, 21 Feb 2006 15:34:25 -0500
Subject: [BiO BB] Tiling microarray
Message-ID: <C020E381.650%chea@mail.nih.gov>

Hi,

Does anyone know how to normalize Tiling microarray data?
And any good software that analysis tiling microarray data.

Thanks,

Anney
-- 
Anney Che, M.S.
Biocomputing Specialist
Laboratory of Molecular Microbiology (LMM)
National Institute of Allergy and Infectious Diseases (NIAID)
9000 Rockville Pike, Bldg 4, Room 301
Bethesda, MD 20892
Phone: 301-451-2851
Fax: 301-280-2716




From aloraine at gmail.com  Tue Feb 21 16:00:05 2006
From: aloraine at gmail.com (Ann Loraine)
Date: Tue, 21 Feb 2006 15:00:05 -0600
Subject: [BiO BB] Tiling microarray
In-Reply-To: <C020E381.650%chea@mail.nih.gov>
References: <C020E381.650%chea@mail.nih.gov>
Message-ID: <83722dde0602211300yf7c8d9bi3d7e917d641e01ed@mail.gmail.com>

This is a just a guess, I'm afraid, but quantile-quantile
normalization is probably a good way to go.

For visualizing tiling array data, I recommend using the Integrated
Genome Browser. It lets you do things like load tiling array data as
simple text files with position/value pairs and then perform simple
manipulations, such as subtracting one graph from another.

There are some links from my Web site http://www.transvar.org
including a now slightly out-of-date tutorial
(http://www.transvar.org/at_annots) that might be useful. Also, you
should check out http://genoviz.sourceforge.net. That will take you to
a Java Web Start page at Affymetrix where you can download and launch
the program.

All the best,

Ann Loraine

On 2/21/06, Che, Anney (NIHNIAID) <chea at mail.nih.gov> wrote:
> Hi,
>
> Does anyone know how to normalize Tiling microarray data?
> And any good software that analysis tiling microarray data.
>
> Thanks,
>
> Anney
> --
> Anney Che, M.S.
> Biocomputing Specialist
> Laboratory of Molecular Microbiology (LMM)
> National Institute of Allergy and Infectious Diseases (NIAID)
> 9000 Rockville Pike, Bldg 4, Room 301
> Bethesda, MD 20892
> Phone: 301-451-2851
> Fax: 301-280-2716
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>


--
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org


From maximilianh at gmail.com  Tue Feb 21 17:18:41 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Tue, 21 Feb 2006 23:18:41 +0100
Subject: [BiO BB] collecting all genes with a given GO id or its child
	terms
In-Reply-To: <83722dde0602211222l30f0c88cye4e5aeae29d81d45@mail.gmail.com>
References: <83722dde0602211222l30f0c88cye4e5aeae29d81d45@mail.gmail.com>
Message-ID: <76f031ae0602211418o388b84abq@mail.gmail.com>

I wonder if you couldn't simply download the arabidopsis GO from
ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20060218.txt,
import it into (wouuw...) Excel and filter by the 4th field (=GO id)...? The
1st fields would then contain the corresponding gene id.

Oh. You're not a biologist. So replace Excel by BioPerl or Python or AWK.
:-)

Take care,
Max

On 21/02/06, Ann Loraine <aloraine at gmail.com> wrote:
>
> Hi,
>
> Maybe somebody on the list could point me in the right direction?
>
> I'm looking for something that takes a list of GO ids and then returns
> a list of all Arabidopsis 'AGI' codes (gene ids, e.g., AT4G30490 )
> that have been annotated with a GO id on the list and/or the child
> term of any GO term on the list.
>
> All the best,
>
> Ann Loraine
>
> --
> Ann Loraine
> Assistant Professor
> Section on Statistical Genetics
> University of Alabama at Birmingham
> http://www.ssg.uab.edu
> http://www.transvar.org
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>



--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler
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From wusu at ele.uri.edu  Tue Feb 21 18:49:17 2006
From: wusu at ele.uri.edu (wusu at ele.uri.edu)
Date: Tue, 21 Feb 2006 18:49:17 -0500
Subject: [BiO BB] Mean and Standard deviation
In-Reply-To: <bdd10c2a0602210917g70edb384l5d1a6328629f0a2b@mail.gmail.com>
References: <20060221050325.25235.qmail@web31501.mail.mud.yahoo.com>
	<70C50B8807B54A429AC206E83A3BA6BCAD8C5C@mail.nymc.edu>
	<bdd10c2a0602210917g70edb384l5d1a6328629f0a2b@mail.gmail.com>
Message-ID: <1140565757.43fba6fda4f5c@webmail.ele.uri.edu>

The mathematical interpretations for the reduction of SD due to a trimmed sample
size at both ends are all very good. However, I don't know why you would get
rid of the end points of your data set, because the frequencies for both end
classes or points are rather high (that is 85 + 33 = 118) compared with the
other classes. You are ignoring 118 / 394 = 29.95% of your data set. If it is
the boundary effect that you are concerned with, you may want to redesign the
experiment or simulation in my opinion.
Regards,
Su

Quoting Martin Gollery <marty.gollery at gmail.com>:

> Chris is correct. Another way to look at it is to consider that you are
> removing the values that have the greatest deviation from the mean, and so
> it makes sense that you then have a lower standard deviation.
> 
> Marty
> 
> On 2/21/06, Frenz, Christopher <CHRISTOPHER_FRENZ at nymc.edu> wrote:
> >
> > SD calculations involve the sample size as one of the variables.  This is
> > likely what is causing the change in SD, since you are reducing the the
> > sample size when you remove the two sets of endpoints.
> >
> > Chris
> >
> >
> > -----Original Message-----
> > From: bio_bulletin_board-bounces+christopher_frenz=
> > nymc.edu at bioinformatics.org on behalf of Subhash Agarwal
> > Sent: Tue 2/21/2006 12:03 AM
> > To: bioinformatics.org
> > Subject: [BiO BB] Mean and Standard deviation
> >
> > Dear Forum Memebers
> >
> >   I have a dataset with 394 data points. The frequecy distribution of
> > which is as follows:
> >
> >                 0-0.02  85    0.02-0.04  63    0.04-0.06  51    0.06-0.08
> >   39    0.08-0.1  36    0.10-0.12  24    -0.12-0.14  21    0.14-0.16
> >   19    0.16-0.18  13    0.18-0.2  10            >0.20            33
> >
> >   The mean and SD of the data is 0.0842 and 0.0853. But when the data
> > points from 0-0.02 and > 0.2 are removed and the mean and SD is calculated
> > it is found that mean doesnt change much (0.0819) but SD does (0.0472). My
> > query is what can I interpret from this regarding the data.
> >
> >   If any of the forum members feels that this question should be addressed
> > to some other place do let me know.
> >
> >   Thanks
> >   Subhash
> >
> >
> > ---------------------------------
> > Jiyo cricket on Yahoo! India cricket
> > Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
> >
> >
> > _______________________________________________
> > Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
> >
> 
> 
> --
> --
> Martin Gollery
> Associate Director
> Center For Bioinformatics
> University of Nevada at Reno
> Dept. of Biochemistry / MS330
> 775-784-7042
> -----------
> 





From nagesh.chakka at anu.edu.au  Tue Feb 21 21:06:04 2006
From: nagesh.chakka at anu.edu.au (Nagesh Chakka)
Date: Wed, 22 Feb 2006 13:06:04 +1100
Subject: [BiO BB] Designing degenerate primers
Message-ID: <43FBC70C.7000602@anu.edu.au>

Hi all,
I need to design primers to "fish out" the region of interest from 
reptilian genomic sequence. I donot have the reptilian gDNA sequence 
information to design the primer with exact sequence. Hence I thought of 
designing degenerate primers based on the available sequence information 
(eutherian mammal, marsupial, amphibian). Are there any available 
programs which does this kind of primer design or that I need to perform 
a multiple sequence alignment and look for the most conserved region and 
design primer with that.
Any advice is greatly appreciated.
Thanks
Nagesh


From smagarwal at yahoo.com  Tue Feb 21 23:34:44 2006
From: smagarwal at yahoo.com (Subhash Agarwal)
Date: Wed, 22 Feb 2006 04:34:44 +0000 (GMT)
Subject: [BiO BB] Mean and SD
Message-ID: <20060222043444.83585.qmail@web31503.mail.mud.yahoo.com>

Dear Forum Members
   
  I agree with the points suggested by all you. From Ryan I would like to ask that keeping in mind that the data doesnt follow normal distribution what other statistical parameters can be calculated to understand whether the data is meaningful or not.
   
  Secondly can Su explain a bit more regarding his suggestion on "redesign the experiment or simulation in my opinion".
   
  thanks
  Subhash

				
---------------------------------
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
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From ryan.raaum at gmail.com  Wed Feb 22 05:25:01 2006
From: ryan.raaum at gmail.com (Ryan Raaum)
Date: Wed, 22 Feb 2006 05:25:01 -0500
Subject: [BiO BB] Mean and SD
In-Reply-To: <20060222043444.83585.qmail@web31503.mail.mud.yahoo.com>
References: <20060222043444.83585.qmail@web31503.mail.mud.yahoo.com>
Message-ID: <a33f26610602220225j33609f12vd8a09d51d7620585@mail.gmail.com>

Hi Subhash

>
> I agree with the points suggested by all you. From Ryan I would like to
> ask that keeping in mind that the data doesnt follow normal distribution
> what other statistical parameters can be calculated to understand whether
> the data is meaningful or not.
>

I think you'll have to provide some more information on what the data
represent and what in particular you are trying to understand before I could
offer any other suggestions.  (And even then, we may have already reached
the limits of my statistical knowledge, but someone else may be able to
provide some helpful advice).

Best,

-Ryan
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From hershel.safer at weizmann.ac.il  Wed Feb 22 10:22:20 2006
From: hershel.safer at weizmann.ac.il (Hershel Safer)
Date: Wed, 22 Feb 2006 17:22:20 +0200
Subject: [BiO BB] March 15th deadline for European Conf on Computational
	Biology
Message-ID: <7.0.1.0.2.20060222172203.02aafa80@alum.mit.edu>

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From maximilianh at gmail.com  Wed Feb 22 20:56:28 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Thu, 23 Feb 2006 02:56:28 +0100
Subject: [BiO BB] Designing degenerate primers
In-Reply-To: <43FBC70C.7000602@anu.edu.au>
References: <43FBC70C.7000602@anu.edu.au>
Message-ID: <76f031ae0602221756q37789c80y@mail.gmail.com>

forgot to forward to the list:
you don't have to do the sequences alignment yourself. on
genome-test.soe.ucsc.edu you'll find multiple alignments of 12 mammalian
species (switch on track "MultiZ 10 way" or "MultiZ 12 way"). You can
extract alignments with "Table Browser" - "MultiZ 10 Way" - Download as maf
(or fasta?).

Take care,
Max

On 22/02/06, Nagesh Chakka <nagesh.chakka at anu.edu.au> wrote:
>
> Hi all,
> I need to design primers to "fish out" the region of interest from
> reptilian genomic sequence. I donot have the reptilian gDNA sequence
> information to design the primer with exact sequence. Hence I thought of
> designing degenerate primers based on the available sequence information
> (eutherian mammal, marsupial, amphibian). Are there any available
> programs which does this kind of primer design or that I need to perform
> a multiple sequence alignment and look for the most conserved region and
> design primer with that.
> Any advice is greatly appreciated.
> Thanks
> Nagesh
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>



--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler
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From logan at cacs.louisiana.edu  Fri Feb 24 12:56:35 2006
From: logan at cacs.louisiana.edu (Raja Loganantharaj)
Date: Fri, 24 Feb 2006 11:56:35 -0600
Subject: [BiO BB] Need help on batch query on GO ontology
Message-ID: <43FF48D3.60308@cacs.louisiana.edu>

I have a set of GO IDs for a set of genes and I would like to obtain 
their taxonomical GO hierarchy. The GO portal allow single ID at a time. 
Is there any API or software from which I enter or read in the set of GO 
ID or genes so that I get the clustered output based on their 
function(say). I have tried DAVID.

Thanks and I appreciate you sharing your experience.

Raja Loganantharaj


From idh at poulet.org  Sat Feb 25 11:39:37 2006
From: idh at poulet.org (idh at poulet.org)
Date: Sat, 25 Feb 2006 17:39:37 +0100
Subject: [BiO BB] Need help on batch query on GO ontology
In-Reply-To: <43FF48D3.60308@cacs.louisiana.edu>
References: <43FF48D3.60308@cacs.louisiana.edu>
Message-ID: <1140885577.44008849af80e@webmail.poulet.org>

Hi Raja,

I do not know how much detail you need, but you might want to have a look at a
tool I used recently: wego
   http://wego.genomics.org.cn/


Upload your gene ontology annotation file, and it will tell you how many genes
are in each go category. You can also fold the hierarchy down to a given level
(say level 2 if you want the tool to cumulatively count how many genes are in
each basal category).

Cheers,

Yannick


---
http://www.unil.ch/dee/page28685_en.html

Quoting Raja Loganantharaj <logan at cacs.louisiana.edu>:

> I have a set of GO IDs for a set of genes and I would like to obtain
> their taxonomical GO hierarchy. The GO portal allow single ID at a time.
> Is there any API or software from which I enter or read in the set of GO
> ID or genes so that I get the clustered output based on their
> function(say). I have tried DAVID.
>
> Thanks and I appreciate you sharing your experience.
>
> Raja Loganantharaj
> _______________________________________________
> Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>





From delete at elfdata.com  Sat Feb 25 12:25:27 2006
From: delete at elfdata.com (Theodore H. Smith)
Date: Sat, 25 Feb 2006 17:25:27 +0000
Subject: [BiO BB] BLAST and multiple section alignment
Message-ID: <A100DA46-2132-4EE0-9F40-BD107B9A0E53@elfdata.com>


I'm not sure if I got this correct, so let me know if this isn't  
true. I'm just asking for confirmation here.

My question: It seems that BLAST does not generate multiple section  
alignments? Is this true or not?

By multiple section alignments, I  mean for example when the head of  
a gene is moved to the middle of a gene. A very sophisticated gene  
searcher could generate a stronger hit for such a case, than simply  
returning the best alignment, because there will now be multiple  
alignments within the two genes that we are comparing.

--
http://elfdata.com/plugin/





From bioinfosm at gmail.com  Sun Feb 26 12:57:45 2006
From: bioinfosm at gmail.com (Samantha Fox)
Date: Sun, 26 Feb 2006 12:57:45 -0500
Subject: [BiO BB] mapping genbank accession to Organism name
Message-ID: <726450810602260957h12229647q88a33dab6d5a07ed@mail.gmail.com>

Hi all,
This should be really easy, but somehow I am cannot figure it out. I BLASTed
my sequences with the non-redundant nt sequence from NCBI.
The hits are something like gb|AC167666.4, emb|BX640434.1, emb|BX640418.1
...

Can someone suggest me a way to get the organism name from these genbank
accessions ?

hope someone has done this already :) ..
~S
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From sourangshu at csa.iisc.ernet.in  Mon Feb 27 06:54:37 2006
From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya)
Date: Mon, 27 Feb 2006 17:24:37 +0530 (IST)
Subject: [BiO BB] Extra entries in blast blosum62 matrix
In-Reply-To: <7.0.1.0.2.20060222172203.02aafa80@alum.mit.edu>
References: <7.0.1.0.2.20060222172203.02aafa80@alum.mit.edu>
Message-ID: <Pine.LNX.4.61.0602271722090.18239@sapphire.csa.iisc.ernet.in>

Hi,

Just wondering what the B, Z, and X entries in blast blosum 62 matrix 
mean.. Any idea ??

Thanks,

Sourangshu

Sourangshu Bhattacharya
PhD Student,
Dept. of Computer Science & Automation,
IISc, Bangalore.

http://people.csa.iisc.ernet.in/sourangshu




From golharam at umdnj.edu  Sun Feb 26 13:20:22 2006
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sun, 26 Feb 2006 13:20:22 -0500
Subject: [BiO BB] mapping genbank accession to Organism name
In-Reply-To: <726450810602260957h12229647q88a33dab6d5a07ed@mail.gmail.com>
Message-ID: <012301c63b01$4efc9520$e6028a0a@GOLHARMOBILE1>

Use the NCBI eutils.  Submit the GenBank accession # to get the GenBank
record in XML.  The XML record will contain an entry for the organism.

Here's a script I have to do this.  First input is the database,
nucleotide in your case, search term is the accession #.  No options
causes the results to be sent back in ASN.1 format.  I forget the option
to make it xml.  I think its rettype=XML or something like that.
 
You can even put your input in a text file and redirect the file as
input to the script...
 
 
---BEGIN: efetch.pl---
#!/usr/bin/perl -w
 
use LWP::Simple;
 
my $utils = " <http://eutils.ncbi.nlm.nih.gov/entrez/eutils>
http://eutils.ncbi.nlm.nih.gov/entrez/eutils";
 
print "Database: ";
$db = <STDIN>;
chomp $db;
 
print "Search Term: ";
$term = <STDIN>;
chomp $term;
 
print "Options: ";
$options = <STDIN>;
chomp $options;
 
my $esearch =
"$utils/esearch.fcgi?db=$db&term=$term&usehistory=y&tool=efetch";
print "$esearch\n";
my $esearch_result = get($esearch);
 
if ($esearch_result =~ m/<Id>(\d+)<\/Id>/) {
        $id = $1;
}
if ($esearch_result =~ m/<QueryKey>(\d+)<\/QueryKey>/) {
        $key = $1;
}
if ($esearch_result =~ m/<WebEnv>(.*)<\/WebEnv>/) {
        $webenv = $1;
}
 
if (defined($id)) {
        print "ID: $id\nKey: $key\nWebEnv: $webenv\n\n";
 
        $esearch = "$utils/efetch.fcgi?db=$db&id=$id&tool=efetch";
        print "$esearch\n";
        my $esummary_result = get($esearch);
        print "$esummary_result\n";
} else {
        print "$esearch_result\n";
}
---END: efetch.ph---
 

-----Original Message-----
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of Samantha Fox
Sent: Sunday, February 26, 2006 12:58 PM
To: The general forum at Bioinformatics.Org
Subject: [BiO BB] mapping genbank accession to Organism name


Hi all,
This should be really easy, but somehow I am cannot figure it out. I
BLASTed my sequences with the non-redundant nt sequence from NCBI.
The hits are something like gb|AC167666.4, emb|BX640434.1,
emb|BX640418.1 ...

Can someone suggest me a way to get the organism name from these genbank
accessions ?

hope someone has done this already :) ..
~S


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From MEC at Stowers-Institute.org  Thu Feb 23 11:41:39 2006
From: MEC at Stowers-Institute.org (Cook, Malcolm)
Date: Thu, 23 Feb 2006 10:41:39 -0600
Subject: [BiO BB] Designing degenerate primers
Message-ID: <CED81D34E37D5043A1211565277A51E504D2D5DC@exchkc02.stowers-institute.org>

Nagesh,
 
Vector NTI's  (windows only) AlignX module supports your needs quite
nicely (though not in a high throughput fashion).  Version 10 is now
free to academics (!), though getting registered is a bit of a bear.  
 
Some researchers here at the Stowers Institute used it for amping up a
lizard gene based on chicken aligned with (was it?) mouse.  For further
specificity, they designed nested degenerate primer pairs (if I remember
correctly).
 
AlignX can import precomputed alignments too (but only in MAF format).
 
Let us know what you do.
 
The following is from their Help file, and might help you decide if the
weighty install is worth your effort:
 

	The Alignment PCR feature in Vector NTI allows you to design PCR
primers for amplifying a region of aligned DNA/RNA molecules. Using this
feature, you can design primer pair sets that will amplify any of the
DNA/RNA molecules in a specified alignment. In this type of PCR
analysis, the molecules are first aligned in AlignX and the alignment is
subsequently analyzed using the Alignment PCR feature in Vector NTI.
	The basic procedure for performing an Alignment PCR analysis
consists of the following steps:
	 
	1. Define the set of DNA/RNA molecules you want to use for
Alignment PCR analysis.
	 
	2. Align the set of molecules in AlignX.
	 
	3. Select a region of the AlignX alignment for which Alignment
PCR will be run.
	 
	4. Define the Alignment PCR parameters.
	 
	5. Perform the Alignment PCR analysis.
	 

>From another page in the help file (Alignment PCR parameters), I quote
additionally:
 

	Primer/Every Molecule Set the minimum overall similarity and 3'
end similarity for the primer with every molecule in the alignment

Cheers,

Malcolm Cook - mec at stowers-institute.org
<mailto:mec at stowers-institute.org>  - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA 




 


	
________________________________

	From:
bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformat
ics.org] On Behalf Of Maximilian Haeussler
	Sent: Wednesday, February 22, 2006 7:56 PM
	To: The general forum at Bioinformatics.Org
	Subject: Re: [BiO BB] Designing degenerate primers
	
	
	
	forgot to forward to the list: 
	you don't have to do the sequences alignment yourself. on
genome-test.soe.ucsc.edu <http://genome-test.soe.ucsc.edu/> you'll find
multiple alignments of 12 mammalian species (switch on track "MultiZ 10
way" or "MultiZ 12 way"). You can extract alignments with "Table
Browser" - "MultiZ 10 Way" - Download as maf (or fasta?). 
	
	Take care,
	Max
	
	
	On 22/02/06, Nagesh Chakka < nagesh.chakka at anu.edu.au
<mailto:nagesh.chakka at anu.edu.au> > wrote: 

		Hi all,
		I need to design primers to "fish out" the region of
interest from 
		reptilian genomic sequence. I donot have the reptilian
gDNA sequence
		information to design the primer with exact sequence.
Hence I thought of
		designing degenerate primers based on the available
sequence information 
		(eutherian mammal, marsupial, amphibian). Are there any
available
		programs which does this kind of primer design or that I
need to perform
		a multiple sequence alignment and look for the most
conserved region and 
		design primer with that.
		Any advice is greatly appreciated.
		Thanks
		Nagesh
		_______________________________________________
		Bioinformatics.Org general forum  -
BiO_Bulletin_Board at bioinformatics.org
<mailto:BiO_Bulletin_Board at bioinformatics.org> 
	
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
<https://bioinformatics.org/mailman/listinfo/bio_bulletin_board> 
		




	-- 
	Maximilian Haeussler, 
	CNRS Gif-sur-Yvette, Paris
	tel: +33 6 12 82 76 16
	icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
<mailto:maximilian.haeussler at hpi.uni-potsdam.de>  
	skype: maximilianhaeussler 

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From maximilianh at gmail.com  Mon Feb 27 08:47:51 2006
From: maximilianh at gmail.com (Maximilian Haeussler)
Date: Mon, 27 Feb 2006 14:47:51 +0100
Subject: [BiO BB] Designing degenerate primers
In-Reply-To: <76f031ae0602221756q37789c80y@mail.gmail.com>
References: <43FBC70C.7000602@anu.edu.au>
	<76f031ae0602221756q37789c80y@mail.gmail.com>
Message-ID: <76f031ae0602270547x4c0a1744v@mail.gmail.com>

To import sequences into vector NTI:
Yes, you can download the alignments from ucsc directly, but only in
maf-format. If you need them converted to fasta, you can do it manually if
it's only a few sequences (search-replace) or use a script maf2fasta which
does to conversion for you. (if you cannot find it, I also have written
python script that does it)

I quote from the genome-mailinglist at ucsc:


Hi Robert,

You may try the download the multiz program from:
http://www.bx.psu.edu/miller_lab/dist/multiz-tba-2005-04-28.tar.gz. In there
you can find a program called maf2fasta, which can convert MAF to FASTA
format.

regards,
Hong

----- Original Message -----
From: "Donna Karolchik" <donnak at soe.ucsc.edu
<http://www.soe.ucsc.edu/mailman/listinfo/genome>>
To: "Querfurth" <querfurt at molgen.mpg.de
<http://www.soe.ucsc.edu/mailman/listinfo/genome>>; <genome at
soe.ucsc.edu <http://www.soe.ucsc.edu/mailman/listinfo/genome>>
Sent: Friday, July 22, 2005 2:59 PM
Subject: Re: [Genome] MAF format


On 23/02/06, Maximilian Haeussler <maximilianh at gmail.com> wrote:
>
> forgot to forward to the list:
> you don't have to do the sequences alignment yourself. on genome-test.soe.ucsc.edu
> you'll find multiple alignments of 12 mammalian species (switch on track
> "MultiZ 10 way" or "MultiZ 12 way"). You can extract alignments with "Table
> Browser" - "MultiZ 10 Way" - Download as maf (or fasta?).
>
> Take care,
> Max
>
> On 22/02/06, Nagesh Chakka < nagesh.chakka at anu.edu.au> wrote:
> >
> > Hi all,
> > I need to design primers to "fish out" the region of interest from
> > reptilian genomic sequence. I donot have the reptilian gDNA sequence
> > information to design the primer with exact sequence. Hence I thought of
> > designing degenerate primers based on the available sequence information
> >
> > (eutherian mammal, marsupial, amphibian). Are there any available
> > programs which does this kind of primer design or that I need to perform
> > a multiple sequence alignment and look for the most conserved region and
> >
> > design primer with that.
> > Any advice is greatly appreciated.
> > Thanks
> > Nagesh
> > _______________________________________________
> > Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
>
>
>
> --
> Maximilian Haeussler,
> CNRS Gif-sur-Yvette, Paris
> tel: +33 6 12 82 76 16
> icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
> skype: maximilianhaeussler




--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
icq: 3825815  -- msn: maximilian.haeussler at hpi.uni-potsdam.de
skype: maximilianhaeussler
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From wusu at ele.uri.edu  Mon Feb 27 12:55:51 2006
From: wusu at ele.uri.edu (wusu at ele.uri.edu)
Date: Mon, 27 Feb 2006 12:55:51 -0500
Subject: [BiO BB] Mean and SD
In-Reply-To: <20060222043444.83585.qmail@web31503.mail.mud.yahoo.com>
References: <20060222043444.83585.qmail@web31503.mail.mud.yahoo.com>
Message-ID: <1141062951.44033d27d2882@webmail.ele.uri.edu>

Dear Subhash and other interested members:

I am sorry for a late reply. I did type up my reply last Thursday, but the
network went dead as I sent it. I just came back from a conference so let me
try to answer the question again. Thank you for your patience!

I am a biomedical engineer that also teaches undergraduate statistics, so I get
to know some statistics. In order to trim down the discarded portion of the
data set, you may decrease the class width from .02 to .01 and then abandon the
end classes. Since we don't have your original data set, it's hard to tell from
a frequency histogram.

Thanks to the beautiful Central Limit Theorem 
so we know that the sampling (or probability) distribution of the sample means
becomes normal if the sample size grows large.

Your sample size was 394 so it's plenty large. Your 394 data values produces
one sample mean, which is only one value of many 'possible' sample means if you
repeat the measurements 394 times over, over and over again. For example, see
http://www.statsoft.com/textbook/stnonpar.html#when

That is to say if you repeat the same experiment many times, the probability
distribution of all the sample means will look normal. Since we don't do such
stupid things, we can really appreciate the word, 'possible' from random
sampling.

Redesign experiments can mean to treat physical boundary problems carefully so
you won't have to throw so many values away. It also applies to simulations, in
which boundary conditions have to be met. I had to do something similar for a
bioelectromagnetics project. Since I don't know what this data set is about, I
can't say much about it. In statistics, experimental design or DOE can mean
different things. You can take a look at a statictics book for
reference or see
http://www.itl.nist.gov/div898/handbook/pri/pri.htm

Perhaps some statistician may respond to us free of charge.
Best regards,
Su Wu - her 2 cents. :)

Quoting Subhash Agarwal <smagarwal at yahoo.com>:

> Dear Forum Members
>    
>   I agree with the points suggested by all you. From Ryan I would like to ask
> that keeping in mind that the data doesnt follow normal distribution what
> other statistical parameters can be calculated to understand whether the data
> is meaningful or not.
>    
>   Secondly can Su explain a bit more regarding his suggestion on "redesign
> the experiment or simulation in my opinion".
>    
>   thanks
>   Subhash
> 
> 				
> ---------------------------------
>  Jiyo cricket on Yahoo! India cricket
> Yahoo! Messenger Mobile Stay in touch with your buddies all the time.





From zhong.huang at jefferson.edu  Tue Feb 28 00:41:40 2006
From: zhong.huang at jefferson.edu (Zhong Huang)
Date: Tue, 28 Feb 2006 00:41:40 -0500
Subject: [BiO BB] fasta to harsh table bioperl
Message-ID: <20060228054128.1CC2C368D42@primary.bioinformatics.org>

hi, 

Can anyone suggest me a simple way to convert multiple sequences fasta 
(in Bio::SeqIO object) into harsh table (sequence annotation as key, 
sequence as value)? 


The fasta file looks like this: 



>gi|9049352|dbj|BAA99407.1| 3-methylcrotonyl-CoA carboxylase
biotin-containing subunit [Homo sapiens] 
MAAASAVSVLLVAAERNRWHRLPSLLLPPRTWVWRQRTMKYTTATGRNITKVLIANRGEIACRVMRTAKKLGVQT-
VAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLSMEKIIQVAKTSAAQAIHPGCGFLSENMEFAE 


>gi|4504067|ref|NP_002070.1| aspartate aminotransferase 1 [Homo sapiens] 
MAPPSVFAEVPQAQPVLVFKLTADFREDPDPRKVNLGVGAYRTDDCHPWVLPVVKKVEQKIANDNSLNHEYLPIL-
GLAEFRSCASRLALGD 

I want to have the harsh table %seqharsh to hold sequences like this: 


#       my %seqharsh = ('seq1', MAAASAVSVL......', 
#                          'seq2', MAPPSVFAEVPQ......,); 


My code is like this: 


my $seqio = new Bio::SeqIO(-format => $format, 
                                 -file   => $file); 


while ( my $seq = $seqio->next_seq ) { 
  if( $seq->alphabet ne 'protein' ) { 
                confess("Skipping non protein sequence..."); 
                next; 
  } 


#write code here to assign each entry into harsh %seqharsh 
        my $seqharsh{$seq->primary_id} = $seq->seq(); 
                bla bla bla 


Thank you very much for your help! 


zhong 





From biopctgi at yahoo.es  Tue Feb 28 05:52:02 2006
From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza)
Date: Tue, 28 Feb 2006 11:52:02 +0100
Subject: [BiO BB] MrBayes - Memory overflow
Message-ID: <44042B52.1090608@yahoo.es>

Hello everyone.

Does anybody know how i could limit the memory usage while creating a 
consensus tree with MrBayes? (even though i am using a 2GB RAM computer)

The problem (segmentation fault) only appears when i'm trying to build a 
tree with more than 40 taxa, so the problem is not in the compilation, 
nor in the commands given.

my mrbayes command is:
sumt filename=filewithALLtrees contype=allcompat burnin=1500

Many thanks in advance.

Regards,
Txema



From omoya at uib.es  Tue Feb 28 06:40:41 2006
From: omoya at uib.es (Oscar Moya)
Date: Tue, 28 Feb 2006 12:40:41 +0100
Subject: [BiO BB] MrBayes - Memory overflow
In-Reply-To: <44042B52.1090608@yahoo.es>
Message-ID: <01LZI35E3X6C8ZET1I@uib.es>

Hi Txema,

I am not sure about if your problem is due to memory needs. I am running
analyses of 70 sequences 1200 bases long in 512MB RAM computers.

Have you tried to run it on another computer? It sounds evident, but
sometimes work.

If problems keep, you could send the command block for checking (mcmc
settings, Lset, prset, etc...).

Good luck!

?scar

-----Mensaje original-----
De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
nombre de Jose Maria Gonzalez Izarzugaza
Enviado el: martes, 28 de febrero de 2006 11:52
Para: bio_bulletin_board at bioinformatics.org
Asunto: [BiO BB] MrBayes - Memory overflow

Hello everyone.

Does anybody know how i could limit the memory usage while creating a 
consensus tree with MrBayes? (even though i am using a 2GB RAM computer)

The problem (segmentation fault) only appears when i'm trying to build a 
tree with more than 40 taxa, so the problem is not in the compilation, 
nor in the commands given.

my mrbayes command is:
sumt filename=filewithALLtrees contype=allcompat burnin=1500

Many thanks in advance.

Regards,
Txema

_______________________________________________
Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From biopctgi at yahoo.es  Tue Feb 28 06:53:05 2006
From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza)
Date: Tue, 28 Feb 2006 12:53:05 +0100
Subject: [BiO BB] MrBayes - Memory overflow
In-Reply-To: <01LZI35E3X6C8ZET1I@uib.es>
References: <01LZI35E3X6C8ZET1I@uib.es>
Message-ID: <440439A1.8050006@yahoo.es>

Thanks a lot, Oscar.

I've tried to run the consensus tree on different computers, with 
different architechtures, and the results are the same in all of them: a 
"nice" segmentation fault after reading the 2 tree files. The problem is 
just with one specific dataset, the one with the most taxa. That's why i 
say it migth be due to memory limitations.

As i use a previously generated set of trees, the command block is as 
simple as

sumt filename=filewithALLtrees contype=allcompat burnin=1500 (where contype can also be skipped to the default half compat)

----------------------------------------------------------------------------------------------------------------------------------------- 


Oscar Moya wrote:

>Hi Txema,
>
>I am not sure about if your problem is due to memory needs. I am running
>analyses of 70 sequences 1200 bases long in 512MB RAM computers.
>
>Have you tried to run it on another computer? It sounds evident, but
>sometimes work.
>
>If problems keep, you could send the command block for checking (mcmc
>settings, Lset, prset, etc...).
>
>Good luck!
>
>?scar
>
>-----Mensaje original-----
>De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
>[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
>nombre de Jose Maria Gonzalez Izarzugaza
>Enviado el: martes, 28 de febrero de 2006 11:52
>Para: bio_bulletin_board at bioinformatics.org
>Asunto: [BiO BB] MrBayes - Memory overflow
>
>Hello everyone.
>
>Does anybody know how i could limit the memory usage while creating a 
>consensus tree with MrBayes? (even though i am using a 2GB RAM computer)
>
>The problem (segmentation fault) only appears when i'm trying to build a 
>tree with more than 40 taxa, so the problem is not in the compilation, 
>nor in the commands given.
>
>my mrbayes command is:
>sumt filename=filewithALLtrees contype=allcompat burnin=1500
>
>Many thanks in advance.
>
>Regards,
>Txema
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>  
>



From omoya at uib.es  Tue Feb 28 09:29:38 2006
From: omoya at uib.es (Oscar Moya)
Date: Tue, 28 Feb 2006 15:29:38 +0100
Subject: [BiO BB] MrBayes - Memory overflow
In-Reply-To: <440439A1.8050006@yahoo.es>
Message-ID: <01LZI91W1IO28ZET1I@uib.es>


Ok, commands and computer discarded

I have just seen that MrBayes has problems with 64 bit architechtures, don?t
know if you have tried in 32 bits one. The following links speak about
similar cases:

http://sourceforge.net/mailarchive/forum.php?thread_id=9725904&forum_id=4511
7

http://www.rannala.org/phpBB2/search.php?search_author=GertW&


A solution for some of them was to download the sourcecode from CVS at
Sourceforge and compile it by themselves. 

Hope that helps

?scar


-----Mensaje original-----
De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
nombre de Jose Maria Gonzalez Izarzugaza
Enviado el: martes, 28 de febrero de 2006 12:53
Para: The general forum at Bioinformatics.Org
Asunto: Re: [BiO BB] MrBayes - Memory overflow

Thanks a lot, Oscar.

I've tried to run the consensus tree on different computers, with 
different architechtures, and the results are the same in all of them: a 
"nice" segmentation fault after reading the 2 tree files. The problem is 
just with one specific dataset, the one with the most taxa. That's why i 
say it migth be due to memory limitations.

As i use a previously generated set of trees, the command block is as 
simple as

sumt filename=filewithALLtrees contype=allcompat burnin=1500 (where contype
can also be skipped to the default half compat)

----------------------------------------------------------------------------
------------------------------------------------------------- 


Oscar Moya wrote:

>Hi Txema,
>
>I am not sure about if your problem is due to memory needs. I am running
>analyses of 70 sequences 1200 bases long in 512MB RAM computers.
>
>Have you tried to run it on another computer? It sounds evident, but
>sometimes work.
>
>If problems keep, you could send the command block for checking (mcmc
>settings, Lset, prset, etc...).
>
>Good luck!
>
>?scar
>
>-----Mensaje original-----
>De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
>[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
>nombre de Jose Maria Gonzalez Izarzugaza
>Enviado el: martes, 28 de febrero de 2006 11:52
>Para: bio_bulletin_board at bioinformatics.org
>Asunto: [BiO BB] MrBayes - Memory overflow
>
>Hello everyone.
>
>Does anybody know how i could limit the memory usage while creating a 
>consensus tree with MrBayes? (even though i am using a 2GB RAM computer)
>
>The problem (segmentation fault) only appears when i'm trying to build a 
>tree with more than 40 taxa, so the problem is not in the compilation, 
>nor in the commands given.
>
>my mrbayes command is:
>sumt filename=filewithALLtrees contype=allcompat burnin=1500
>
>Many thanks in advance.
>
>Regards,
>Txema
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>  
>

_______________________________________________
Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board




From biopctgi at yahoo.es  Tue Feb 28 09:52:45 2006
From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza)
Date: Tue, 28 Feb 2006 15:52:45 +0100
Subject: [BiO BB] MrBayes - Memory overflow
In-Reply-To: <01LZI91W1IO28ZET1I@uib.es>
References: <01LZI91W1IO28ZET1I@uib.es>
Message-ID: <440463BD.9010504@yahoo.es>

Many thanks.
Txema

Oscar Moya wrote:

>Ok, commands and computer discarded
>
>I have just seen that MrBayes has problems with 64 bit architechtures, don?t
>know if you have tried in 32 bits one. The following links speak about
>similar cases:
>
>http://sourceforge.net/mailarchive/forum.php?thread_id=9725904&forum_id=4511
>7
>
>http://www.rannala.org/phpBB2/search.php?search_author=GertW&
>
>
>A solution for some of them was to download the sourcecode from CVS at
>Sourceforge and compile it by themselves. 
>
>Hope that helps
>
>?scar
>
>
>-----Mensaje original-----
>De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
>[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
>nombre de Jose Maria Gonzalez Izarzugaza
>Enviado el: martes, 28 de febrero de 2006 12:53
>Para: The general forum at Bioinformatics.Org
>Asunto: Re: [BiO BB] MrBayes - Memory overflow
>
>Thanks a lot, Oscar.
>
>I've tried to run the consensus tree on different computers, with 
>different architechtures, and the results are the same in all of them: a 
>"nice" segmentation fault after reading the 2 tree files. The problem is 
>just with one specific dataset, the one with the most taxa. That's why i 
>say it migth be due to memory limitations.
>
>As i use a previously generated set of trees, the command block is as 
>simple as
>
>sumt filename=filewithALLtrees contype=allcompat burnin=1500 (where contype
>can also be skipped to the default half compat)
>
>----------------------------------------------------------------------------
>------------------------------------------------------------- 
>
>
>Oscar Moya wrote:
>
>  
>
>>Hi Txema,
>>
>>I am not sure about if your problem is due to memory needs. I am running
>>analyses of 70 sequences 1200 bases long in 512MB RAM computers.
>>
>>Have you tried to run it on another computer? It sounds evident, but
>>sometimes work.
>>
>>If problems keep, you could send the command block for checking (mcmc
>>settings, Lset, prset, etc...).
>>
>>Good luck!
>>
>>?scar
>>
>>-----Mensaje original-----
>>De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
>>[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
>>nombre de Jose Maria Gonzalez Izarzugaza
>>Enviado el: martes, 28 de febrero de 2006 11:52
>>Para: bio_bulletin_board at bioinformatics.org
>>Asunto: [BiO BB] MrBayes - Memory overflow
>>
>>Hello everyone.
>>
>>Does anybody know how i could limit the memory usage while creating a 
>>consensus tree with MrBayes? (even though i am using a 2GB RAM computer)
>>
>>The problem (segmentation fault) only appears when i'm trying to build a 
>>tree with more than 40 taxa, so the problem is not in the compilation, 
>>nor in the commands given.
>>
>>my mrbayes command is:
>>sumt filename=filewithALLtrees contype=allcompat burnin=1500
>>
>>Many thanks in advance.
>>
>>Regards,
>>Txema
>>
>>_______________________________________________
>>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>>
>>_______________________________________________
>>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>>
>> 
>>
>>    
>>
>
>_______________________________________________
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
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From MAG at Stowers-Institute.org  Tue Feb 28 15:51:36 2006
From: MAG at Stowers-Institute.org (Goel, Manisha)
Date: Tue, 28 Feb 2006 14:51:36 -0600
Subject: [BiO BB] Energy minimazation program
Message-ID: <C28BAF593DC3314E9C0F3A50191C2E7802B4E885@EXCHKC03.stowers-institute.org>


Hi All,

I have a simple problem, I hope someone can advice.
I needed to make a covalent bond between a sugar molecule and an
aminoacid
>(aa-COOH + sugar-OH --> H2O + aa-sugar).
I had them in a single pdb file and managed to generate a pdb file with
a covalent bond, but the geometry of this resulting molecule is very
distorted.
I now need to optimize this geometry and I think that energy
minimization shouwl be able to take care of that.
I have previously used insightII for this energy minimization but do not
access to it anymore.
Is there any software avaibale (free for academic use) that should be
able to do this.
I did a google search and find quite a few but cannot decide which one
to start with, because each would have a learning curve.
Please suggest something that you think is more popular/optimal. 

Thanks for any help.
-Manisha Goel

Post-doc associate
Stowers Institute for Medical Research
1000 E 50th St.
Kansas city, 64110


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