From christoph.gille at charite.de Wed Feb 9 06:49:42 2005
From: christoph.gille at charite.de (Dr. Christoph Gille)
Date: Wed, 9 Feb 2005 12:49:42 +0100 (MET)
Subject: [BiO BB] MacOSx : I need to compile some programs
Message-ID: <34103.141.42.56.114.1107949782.squirrel@webmail.charite.de>
I am developing STRAP
STRAP, program for protein alignments.
It uses many other programs.
Some of them are written in C/C++ and must
be compiled for all different target machines.
If you have a Mac OSX, could you please compile a few programs.
This should not take long, because they have Makefiles.
Or does somebody know how I can make executables for Mac
using my linux i386 computer ?
Thanks for your help
Christoph
From virajj at lycos.com Wed Feb 9 18:23:56 2005
From: virajj at lycos.com (vijaya raj)
Date: Wed, 09 Feb 2005 18:23:56 -0500
Subject: [BiO BB] sign-against-software-patents
Message-ID: <20050209232356.09453E5BC7@ws7-2.us4.outblaze.com>
hi guys...
the european commission is trying to legalise software
patents..which means...un-imaginable consequences...
chek out here..
please sign against this dangerous venture....pass it on to your friends...
http://www.noepatents.org/index_html?LANG=en
read this article...knoppix under threat...
http://www.knoppix.org/
do sign against this monster attempt...
vijay
--
_______________________________________________
Find what you are looking for with the Lycos Yellow Pages
http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10
From Susan_Braunhut at uml.edu Thu Feb 10 17:15:50 2005
From: Susan_Braunhut at uml.edu (Susan Braunhut)
Date: Thu, 10 Feb 2005 17:15:50 -0500
Subject: [BiO BB] Bioinformatics Conference- Keynotes,
Exciting New Research-Free
Message-ID: <002401c50fbe$14e85320$6501a8c0@shiloh>
Laboratories of Innovation:
Bioinformatics at
The University of Massachusetts
April 29th, 2005
8:30 AM- 5:00 PM
with a reception following the conference
Please join us for a day conference highlighting the innovative work in bioinformatics taking place on the five campuses of the University of Massachusetts
Keynote speakers
Dr. John N. Weinstein, M.D., Ph.D.
Head, Genomics & Bioinformatics Group,
LMP, CCR, National Cancer Institute
Dr. Mark Gerstein, Ph.D.
Associate Professor of Biomedical Informatics,
Yale University
Attendance is free but registration is limited
Lunch and reception will be provided
Deadline for registration is April 15th, 2005.
Register at:
http://cs.uml.edu/ivpr/meeting.html
For additional information contact Dr. Georges Grinstein
978-934-3627 or grinstein at cs.uml.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From nuraini at cs.usm.my Wed Feb 16 04:01:27 2005
From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid)
Date: Wed, 16 Feb 2005 17:01:27 +0800
Subject: [BiO BB] NEIGHBOUR program from PHYLIP suite
References: <1095872087.4151ae57d6da3@hongyu.org>
Message-ID: <001501c51406$1cee0f50$4482cf0a@MyBox2>
Dear All,
I'm trying to generate a phylogenetic tree using NEIGHBOUR, a public domain
program from the PHYLIP software suite... but I get the error the diagonal
element of row 1 of distance matrix is not zero.. but it is zero... When I
try to use upper triangular data matrix I got the message
The infile is of the wrong type..
I created the file using Microsoft.net C ++ software . It is a text file..
Please help.
Nora.
_______________________________________________
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
From idh at poulet.org Fri Feb 18 09:15:56 2005
From: idh at poulet.org (Yannick Wurm)
Date: Fri, 18 Feb 2005 15:15:56 +0100
Subject: [BiO BB] Refined nucleotide BLAST matrix
Message-ID: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
Hi,
for a specific need in my lab, we are looking for an implementation of
nucleotide sequence alignment program which would be more flexible than
standard BLAST.
The reason is that we have sequenced dna fragments which have been
submitted to chemical modifications which differentially affects
different nucleotides.
To help identify these sequences, we need to be able to fine-tune the
matrix used for scoring. Thus, for example when calculating the "score"
of an aligment, C->A and C->T could be given different weights.
According to ebi.ac.uk, the WU-blast matrix is:
A T G C
A 5
T -4 5
G -4 -4 5
C -4 -4 -4 5
We want to be able to specifiy inidividual values to something like the
following example:
A T G C
A 2
T -4 8
G -8 -10 3
C -2 -1 -3 10
To my surprise, BLAST does not have this liberty, despite the fact that
different scoring matrices are used for proteins. I couldn't find
anything on Google either.
Would anyone one the list have a clue? Or do I need to get dirty
messing with BLAST's source?
Thanks in advance,
Yannick
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
From danny at amelang.net Fri Feb 18 12:05:29 2005
From: danny at amelang.net (Daniel Amelang)
Date: Fri, 18 Feb 2005 10:05:29 -0700
Subject: [BiO BB] Refined nucleotide BLAST matrix
In-Reply-To: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
Message-ID: <42162059.5070503@amelang.net>
Hi Yannick,
Forgive me if I misunderstood your question, but I think what you're
looking for is the '-DNAMATRIX=custom_matrix.mat' option of clustalw.
I'm using it for a project of mine and it works great. Let me know if
you need help getting it to work. Sometimes clustalw can be picky about
the format of the matrix.
Dan Amelang
Yannick Wurm wrote:
> Hi,
> for a specific need in my lab, we are looking for an implementation of
> nucleotide sequence alignment program which would be more flexible
> than standard BLAST.
> The reason is that we have sequenced dna fragments which have been
> submitted to chemical modifications which differentially affects
> different nucleotides.
>
> To help identify these sequences, we need to be able to fine-tune the
> matrix used for scoring. Thus, for example when calculating the
> "score" of an aligment, C->A and C->T could be given different weights.
>
> According to ebi.ac.uk, the WU-blast matrix is:
> A T G C
> A 5
> T -4 5
> G -4 -4 5
> C -4 -4 -4 5
>
> We want to be able to specifiy inidividual values to something like
> the following example:
> A T G C
> A 2
> T -4 8
> G -8 -10 3
> C -2 -1 -3 10
>
>
> To my surprise, BLAST does not have this liberty, despite the fact
> that different scoring matrices are used for proteins. I couldn't find
> anything on Google either.
>
> Would anyone one the list have a clue? Or do I need to get dirty
> messing with BLAST's source?
> Thanks in advance,
>
> Yannick
>
> . . . . . . . . . . . . . . . . . .
> yannick.wurm at unil.ch
> +41.21.692.4157
> PhD student, Departement of Ecology and Evolution
> Universit? de Lausanne, Switzerland
> _______________________________________________
> Bioinformatics.Org general forum -
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
From idh at poulet.org Fri Feb 18 12:33:05 2005
From: idh at poulet.org (Yannick Wurm)
Date: Fri, 18 Feb 2005 18:33:05 +0100
Subject: [BiO BB] Refined nucleotide BLAST matrix
In-Reply-To: <42162059.5070503@amelang.net>
References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
<42162059.5070503@amelang.net>
Message-ID: <25C9CB04-81D3-11D9-A931-000D93712582@poulet.org>
Thanks for your feedback Dan,
I guess that could be what I'm looking for. However, I don't want
multiple alignments so I don't think clustal will do the trick.
Basically, I have one interesting sequence for which I would love to
find a homologue in the Honey bee or Drosophila genome. A standard
BLAST does not show a significant homology.
My fragment was submitted to chemical treatment which replaces As by
Cs. My sequence thus has many Cs, some of which were already C in the
original sequence, some of which were As. This makes finding a perfect
alignment difficult. So when scoring the "distance" between my sequence
and a sequence from a genome database, I would like to have a lower
penalty for A-C than for T-C.
Doing this should increase my chance of finding a homologue.
-yannick.
On 18 f?vr. 05, at 18:05, Daniel Amelang wrote:
> Hi Yannick,
>
> Forgive me if I misunderstood your question, but I think what you're
> looking for is the '-DNAMATRIX=custom_matrix.mat' option of clustalw.
> I'm using it for a project of mine and it works great. Let me know if
> you need help getting it to work. Sometimes clustalw can be picky
> about the format of the matrix.
>
> Dan Amelang
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
From pmr at ebi.ac.uk Fri Feb 18 12:40:32 2005
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 18 Feb 2005 17:40:32 +0000
Subject: [BiO BB] Refined nucleotide BLAST matrix
In-Reply-To: <42162059.5070503@amelang.net>
References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
<42162059.5070503@amelang.net>
Message-ID: <42162890.2040205@ebi.ac.uk>
> Yannick Wurm wrote:
>> for a specific need in my lab, we are looking for an implementation of
>> nucleotide sequence alignment program which would be more flexible
>> than standard BLAST.
>>
>> To help identify these sequences, we need to be able to fine-tune the
>> matrix used for scoring. Thus, for example when calculating the
>> "score" of an aligment, C->A and C->T could be given different weights.
>>
>> To my surprise, BLAST does not have this liberty, despite the fact
>> that different scoring matrices are used for proteins. I couldn't find
>> anything on Google either.
>>
>> Would anyone one the list have a clue? Or do I need to get dirty
>> messing with BLAST's source?
Avoid messing with the BLAST sources!
You can get around this - you also need this trick to handle nucleotide
ambiguity codes (for example to compare patent sequences which use codes other
than 'N'.
You have to cheat though.
1. Build your blast database as protein
2. Give your matrix a name that matches one of the blast protein matrix names (!)
3. Put in the matrix values you want
4. Remember that you are now using blastp (protein search) so you can only use
a short wordsize - I am guessing you have short sequences anyway so this
should not be a problem
5. Remember that BLAST does local alignment.
6. Remember that your scores will be making some wrong assumptions about using
proteins. You should still find the hits you are looking for.
This cheat was published (by NCBI if I recall correctly) some time back.
Sorry, I can't track down the reference.
Hope this helps,
Peter Rice
From kalita at rabbit.uccs.edu Mon Feb 14 16:14:52 2005
From: kalita at rabbit.uccs.edu (J. Kalita)
Date: Mon, 14 Feb 2005 14:14:52 -0700 (MST)
Subject: [BiO BB] Announcing BIOT-05: Second Bioinformatics and
Biotechnology Symposium
In-Reply-To: <20041210170009.41E7DD1F2F@www.bioinformatics.org>
References: <20041210170009.41E7DD1F2F@www.bioinformatics.org>
Message-ID: <49813.128.198.172.116.1108415692.squirrel@www.cs.uccs.edu>
Location : Colorado Springs
Symposium Date: August 15-16, 2005
Paper or Abstract Submission Date: March 14, 2005
-------
IOT-05: The Second Biotechnology and Bioinformatics Symposium, will be
held in
Colorado Springs, Colorado on August 15 and 16, 2005. The Web site is
http://bioinfo.uccs.edu . Please click on "Symposium 2005 (BIOT-05)" on
the top left menu to get to the Web site for the symposium.
The symposium's objective is to showcase research and development
activities in:
* Bioinformatics and Computational Biology, and
* Biotechnology
* Impacts of Biotechnology, Bioinformatics and Computational Biology
and to promote future interdisciplinary activity and research in these
areas. Abstracts and papers are solicited in these three areas, broadly
interpreted. Efforts that attempt to solve biology-based problems using
computational, mathematical, engineering and other means are suitable. In
addition, abstracts and papers dealing with community impacts of
Bioinformatics, Computational Biology and Biotechnology are appropriate.
Thus, abstracts and papers in areas such as technology transfer, legal,
business, and social impact issues are also invited.
BIOT-05 will accept abstracts and papers for either podium presentation or
poster presentation. Please look at the Web site for more details. All
submissions of abstracts and papers, whether for podium or poster
presentation, will be reviewed. Printed preceedings will be published
containing all accepted abstracts and papers. You can see a complete copy
of last year's proceedings at
http://bioinfo.uccs.edu/index.php?module=pagemaster&PAGE_user_op=view_page&PAGE_id=49&MMN_position=79:41
.
A partial list of topics for the Symposium include Analysis of complex
biological systems, Artificial or synthetic biological systems,
Bioenergetics, Biomedical research, Biotechnology, Cellular function,
Commercial applications of biotechnology and bioinformatics, Comparative
genomics, Data mining, Databases, Evolution models, Functional genomics,
Genetics, Genomics, High content analysis, High performance computing,
Industrial applications of biotechnolgy and bioinformatics, Legal impacts
of biotechnology and bioinformatics, Mathematical and computational models
of cellular systems, Mathematical models of biophysical processes,
Mathematical physiology, Microarray analysis, Molecular function,
Molecular sequence and structure, Neural circuits modeling, Pathways,
Pattern recognition, Phylogenetics, Physiology, Population biology,
Promoter analysis and discovery, Protein structure and analysis, RNAi
analysis, Sequence alignments, SNPs, Social impacts of bioinformatics and
biotechnology, Systems biology, Technology transfer, Theoretical and
mathematical biology, Venture capital for biotechnolgy and bioinformatics
industry, Visualization.
Like BIOT-04, BIOT-05 will bring together scientists, engineers and other
practitioners from diverse fields. Different fields have different
requirements for conference submissions.
For example, in Computer Science, it is traditional to require submission
of full papers for review several months prior to a conference or
symposium. In Mathematics, often even an abstract is usually not required.
In Biology, usually short abstracts are required. However, most other
fields simply request that an abstract or an extended abstract be
submitted for review.
Since this cross-over meeting will bring together people from fields where
the publishing paradigms is different, authors are encouraged to submit
abstracts, or papers, as appropriate within their subfield. The Symposium
proceedings will contain abstracts as well as papers. The length of your
submission determines the maximum length of your publication in the
proceedings; if you want a paper in the proceedings then you must submit a
paper for review.
Thus, there are two possible ways to participate in BIOT-05. First, you
must decide whether you want to submit
* an extended abstract for review (2 pages) , or
* a full paper for review (up to 6 pages).
An extended abstract or a paper must report significant research results,
findings or advances within its own field. However, since the symposium is
geared toward a diverse audience of biologists, computer scientists,
chemists, engineers, technology transfer individuals, graduate students,
professors, industry individuals, etc., the papers or extended abstracts
must be presented in a lucid manner accessible to such individuals. Please
look at the Web site for more details.
IMPORTANT DATES
* Submission Deadline: March 14, 2005 (Two pages of Extended Abstracts or
6 pages of Full Papers). This may be extended by two or three weeks if
needed.
* Acceptence Decision: April 25, 2005
* Revised Camera Ready Extended Abstracts and Full papers due after
revision: June 6, 2005
* Symposium Date: August 15-16, 2005
Please contact Dr. J. Kalita at jkalita at uccs.edu if you have any questions
about BIOT-05.
From sve02594 at yahoo.com Wed Feb 16 09:45:04 2005
From: sve02594 at yahoo.com (Seema Verma)
Date: Wed, 16 Feb 2005 06:45:04 -0800 (PST)
Subject: [BiO BB] MS computer science(bioinformatics)
Message-ID: <20050216144505.94822.qmail@web50507.mail.yahoo.com>
I am wondering if anyone can suggest me about the
advantage of doing MS computer science with
specialization in bioinformatics. if one has already
PhD in biology(molecular biology). I would appreciate
your rsponse.
Thanks
__________________________________
Do you Yahoo!?
Read only the mail you want - Yahoo! Mail SpamGuard.
http://promotions.yahoo.com/new_mail
From Yannick.Wurm at unil.ch Fri Feb 18 09:13:20 2005
From: Yannick.Wurm at unil.ch (Yannick Wurm)
Date: Fri, 18 Feb 2005 15:13:20 +0100
Subject: [BiO BB] Refined Blast?
Message-ID: <3E591300-81B7-11D9-A931-000D93712582@unil.ch>
Hi,
for a specific need in my lab, we are looking for an implementation of
nucleotide sequence alignment program which would be more flexible than
standard BLAST.
The reason is that we have sequenced dna fragments which have been
submitted to chemical modifications which differentially affects
different nucleotides.
To help identify these sequences, we need to be able to fine-tune the
matrix used for scoring. Thus, for example when calculating the "score"
of an aligment, C->A and C->T could be given different weights.
According to ebi.ac.uk, the WU-blast matrix is:
A T G C
A 5
T -4 5
G -4 -4 5
C -4 -4 -4 5
We want to be able to specifiy inidividual values to something like the
following example:
A T G C
A 2
T -4 8
G -8 -10 3
C -2 -1 -3 10
To my surprise, BLAST does not have this liberty, despite the fact that
different scoring matrices are used for proteins. I couldn't find
anything on Google either.
Would anyone one the list have a clue? Or do I need to get dirty
messing with BLAST's source?
Thanks in advance,
Yannick
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
From maria.mirto at unile.it Sat Feb 19 08:25:12 2005
From: maria.mirto at unile.it (Maria Mirto)
Date: Sat, 19 Feb 2005 14:25:12 +0100 (CET)
Subject: [BiO BB] final CFP: HiPCoMB-2005
Message-ID: <3331.193.204.74.245.1108819512.squirrel@webmail2.unile.it>
********************************************************************************
We apologize if you received multiple copies of this Call for Papers.
Please feel free to distribute it to those who might be interested.
********************************************************************************
___________________________________________________________________
CALL FOR PAPERS
1st IEEE Workshop on High Performance Computing in Medicine and Biology
(HiPCoMB-2005)
held in conjunction with
The 11th International Conference on Parallel and Distributed Systems
(ICPADS 2005)
Fukuoka Institute of Technology (FIT), Fukuoka, Japan
July 20-22, 2005
HiPCoMB-2005 Home Page: http://www.pdcl.wayne.edu/HiPCoMB-2005
(Apologies if you receive multiple copies of this Call for Papers)
_______________________________________________________________________
IMPORTANT DEADLINES:
Paper submission: February 28, 2005
Author Notification: April 07, 2005
Camera-Ready Papers: April 21, 2005
WORKSHOP INFORMATION:
The First Workshop on High Performance Computing in Medicine and
Biology (HiPCoMB-05), held in conjunction with ICPADS 2005 in Fukuoka
City, Japan brings together researchers in computer science and
engineering, medicine, and biology that use high performance computing
to solve computationally expensive problems in medicine and biology.
The workshop will provide a forum for presenting and exchanging new
ideas and experiences in this area.
Topics of interest include high performance algorithms, systems,
architecture, and tools for the following: (but are not limited to the
following list)
* Microarray Analysis
* RNAi Analysis
* Systems Biology
* Computational Genomics
* Comparative Genomics
* DNA Assembly, Clustering, and Mapping
* Gene identification and annotation
* Computational Proteomics
* Evolution and Phylogenetics
* Protein Structure Predication and Modeling
* Medical Image Processing
* Computer Assisted Surgery
* Computational Medicine Modeling
* Computational Biology Modeling
* Augmented Reality
* Medical Informatics
SUBMISSION INFORMATION:
Talks will be accepted on the basis of a paper of approximately 15
single-column pages that describes the work, its significance, and the
current status of the research. Submit one electronic copy of the
paper in PostScript or PDF format by February 15, 2005. Please visit
the workshop home page for submission instructions.
Notification of acceptance will be given by March 22, 2005, and
camera-ready papers will be due April 21, 2005. Accepted papers will
be given guidelines in preparing and submitting the final
manuscript(s) together with the notification of acceptance. All
accepted papers will be presented at the workshop and included in
proceedings that will be distributed at the workshop. In addition,
authors of selected papers from the workshop will be invited to submit
extended versions of their papers for publication in a special issue
of the International Journal of Bioinformatics Research and
Applications.
GENERAL INFORMATION:
GENERAL CO-CHAIRS:
Laurence T. Yang St. Francis Xavier University, Canada
email: lyang at stfx.ca
Albert Zomaya University of Sydney, Australia
email: zomaya at it.usyd.edu.au
PROGRAM CO-CHAIRS:
Vipin Chaudhary Wayne State University, USA
email: vipin at wayne.edu
Andrei Doncescu LAAS, National Center for Scientific
Research,
France
email: adoncesc at laas.fr
Yi Pan Georgia State University, USA
email: pan at cs.gsu.edu
PROGRAM COMMITTEE MEMBERS:
David Abramson, Monash University, Australia
davida at csse.monash.edu.au
Enrique Alba, University of Malaga, Spain
eat at lcc.uma.es
Srinivas Aluru, Iowa State University, USA
aluru at iastate.edu
http://www.ece.iastate.edu/~aluru
Shahid H. Bokhari, University of Engineering & Technology, Pakistan
shb at acm.org
Vincent Breton, CNRS/IN2P3, LPC Clermont-Ferrand, France
breton at clermont.in2p3.fr
Kevin Burrage, University of Queensland, Australia kb at maths.uq.edu.au
Amitava Data, University of Western Australia, Australia
datta at csse.uwa.edu.au
Hans de Sterck, University of Waterloo, Canada
hdesterck at math.uwaterloo.ca
Mario Rosario Guarracino, ICAR-CNR, Italy
mario.guarracino at cps.na.cnr.it
http://pixel.dma.unina.it/~mariog/
Ryoko Hayashi, Advanced Institute of Science and Technology (JAIST),
Japan ryoko at jaist.ac.jp
Matthew He, Nova Southeastern University, USA
hem at nsu.nova.edu
Alfons Hoekstra, University of Amsterdam, The Netherlands
alfons at science.uva.nl
Xiaohua (Tony) Hu, Drexel University, USA
thu at cis.drexel.edu
http://www.cis.drexel.edu/faculty/thu
Chun-Hsi Huang University of Connecticut, USA huang at engr.uconn.edu
Arun Krishnan, Bioinformatics Institute, Singapore
arun at bii.a-star.edu.sg
Joseph Landman, Scalable Informatics, LLC
landman at scalableinformatics.com
Wenjun Li, UT Southwestern Medical Center, USA
liwenjun2k at yahoo.com
Yiming Li, National Chiao Tung University, Taiwan
ymli at mail.nctu.edu.tw
Robert L. Martino, National Institutes of Health, USA
Robert.Martino at nih.gov
Maria Mirto
University of Lecce, Italy
maria.mirto at unile.it
Michael Mascagni, Florida State University, USA
mascagni at fsu.edu
Martin Middendorf, University of Leipzig, Germany
middendorf at informatik.uni-leipzig.de
Giri Narasimhan, Florida International University, USA
giri at cs.fiu.edu
Jun Ni, University of Iowa, USA
jun-ni at uiowa.edu
Sergei Petoukhov, Russian Academy of Sciences, Russia
petoukhov at hotmail.com
Pascal Poulet, French West Indies UNiversity, France
Pascal.Poullet at univ-ag.fr
Youxing Qu, Univresity of Georgia, USA
youxing at csbl.bmb.uga.edu
Nagiza Samatova, Oak Ridge National Lab, USA
samatovan at ornl.gov
Bertil Schmidt, Nanyang Technological University, Singapore
ASBSchmidt at ntu.edu.sg
Tony Solomonides, University of the West of England, UK
Tony.Solomonides at uwe.ac.uk
El-Ghazali Talbi, LIFL, France
talbi at lifl.fr
Daming Wei, University of Aizu, Japan
dm-wei at u-aizu.ac.jp
Tiffani Williams, University of New Mexico, USA
tlw at cs.unm.edu
C. M. Yang, Nankai University, China
yangchm at nankai.edu.cn
Yanqing Zhang, Georgia State University, USA
yzhang at cs.gsu.edu
Bingbing Zhou, University of Sydney, Australia
bbz at it.usyd.edu.au
Information related to ICPADS 2005 is available at the official ICPADS
2005 Web site: http://www.takilab.k.dendai.ac.jp/conf/icpads/2005/
ICPADS 2005 is Co-sponsored by IEEE Computer Society TCDP and TCPP,
and Fukuoka Institute of Technology (FIT), in cooperation with Fukuoka
City, IPSJ (Information Processing Society of Japan) SIGDPS, IEEE
Taipei Section, IEEE HonKong Section, SCAT, and AOARD/AOR.
--
============================================================
Maria Mirto
PhD student, Center for Advanced Computational Technologies
via per Monteroni, 73100 Lecce (Le), ITALY
ph: +39 0832 297304
fax: +39 0832 297279
============================================================
From yogeshshetty2000 at yahoo.com Sun Feb 20 00:28:26 2005
From: yogeshshetty2000 at yahoo.com (yogesh shetty)
Date: Sat, 19 Feb 2005 21:28:26 -0800 (PST)
Subject: [BiO BB] help
Message-ID: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
hello
can any body help me. I need a source code written in java for a clustering tool.
thanking you
---------------------------------
Do you Yahoo!?
Yahoo! Search presents - Jib Jab's 'Second Term'
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
From Yannick.Wurm at unil.ch Mon Feb 21 08:33:38 2005
From: Yannick.Wurm at unil.ch (Yannick Wurm)
Date: Mon, 21 Feb 2005 14:33:38 +0100
Subject: [BiO BB] Refined nucleotide BLAST matrix
In-Reply-To: <42162890.2040205@ebi.ac.uk>
References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org>
<42162059.5070503@amelang.net> <42162890.2040205@ebi.ac.uk>
Message-ID:
Thank you Peter - what a surprising hack!
Thats the way we'll go.
Thanks again,
-yannick
On 18 f?vr. 05, at 18:40, Peter Rice wrote:
>> Yannick Wurm wrote:
>>> for a specific need in my lab, we are looking for an implementation
>>> of nucleotide sequence alignment program which would be more
>>> flexible than standard BLAST.
>>>
>>> To help identify these sequences, we need to be able to fine-tune
>>> the matrix used for scoring. Thus, for example when calculating the
>>> "score" of an aligment, C->A and C->T could be given different
>>> weights.
>>>
>>> To my surprise, BLAST does not have this liberty, despite the fact
>>> that different scoring matrices are used for proteins. I couldn't
>>> find anything on Google either.
>
> You can get around this - you also need this trick to handle
> nucleotide ambiguity codes (for example to compare patent sequences
> which use codes other than 'N'.
>
> You have to cheat though.
>
> 1. Build your blast database as protein
>
> 2. Give your matrix a name that matches one of the blast protein
> matrix names (!)
>
> 3. Put in the matrix values you want
>
> 4. Remember that you are now using blastp (protein search) so you can
> only use a short wordsize - I am guessing you have short sequences
> anyway so this should not be a problem
>
> 5. Remember that BLAST does local alignment.
>
> 6. Remember that your scores will be making some wrong assumptions
> about using proteins. You should still find the hits you are looking
> for.
>
> This cheat was published (by NCBI if I recall correctly) some time
> back. Sorry, I can't track down the reference.
>
> Hope this helps,
>
> Peter Rice
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
From idoerg at burnham.org Mon Feb 21 12:55:07 2005
From: idoerg at burnham.org (Iddo Friedberg)
Date: Mon, 21 Feb 2005 09:55:07 -0800
Subject: [BiO BB] help
In-Reply-To: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
References: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
Message-ID: <421A207B.6030001@burnham.org>
Weka is a machine learning tool in Java which I believe has some
clustering algorithm as well:
http://www.cs.waikato.ac.nz/ml/weka/
./I
yogesh shetty wrote:
> hello
> can any body help me. I need a source code written in java for a
> clustering tool.
>
> thanking you
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! Search presents - Jib Jab's 'Second Term'
>
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
==========================
The First Automated Protein Function Prediction SIG
Detroit, MI June 24, 2005
http://ffas.burnham.org/AFP
From sourangshu at csa.iisc.ernet.in Mon Feb 21 12:48:40 2005
From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya)
Date: Mon, 21 Feb 2005 23:18:40 +0530 (IST)
Subject: [BiO BB] help
In-Reply-To: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
References: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
Message-ID:
Hi,
Check out : www.cs.waikato.ac.nz/ml/weka/
Sourangshu
Sourangshu Bhattacharya
PhD Student,
Dept. of Computer Science & Automation,
IISc, Bangalore.
http://people.csa.iisc.ernet.in/sourangshu
On Sat, 19 Feb 2005, yogesh shetty wrote:
> hello
> can any body help me. I need a source code written in java for a clustering tool.
>
> thanking you
>
>
> ---------------------------------
> Do you Yahoo!?
> Yahoo! Search presents - Jib Jab's 'Second Term'
From milimetr at webmail.cmdik.pan.pl Tue Feb 22 04:01:10 2005
From: milimetr at webmail.cmdik.pan.pl (MACIEJ PIETRZAK)
Date: Tue, 22 Feb 2005 10:01:10 +0100
Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 4, Issue 8
In-Reply-To: <20050221173421.50974D1FE8@www.bioinformatics.org>
References: <20050221173421.50974D1FE8@www.bioinformatics.org>
Message-ID: <20050222085349.M13674@webmail.cmdik.pan.pl>
Hi,
U can also try TESS:
http://www.cbil.upenn.edu/tess/
with your own strings or matrix
Regards
Maciej Pietrzak
dep. of Endocrinology
MRC PAS
WARSAW, POLAND
milimetrcmdik.pan.pl
---------- Original Message -----------
From: bio_bulletin_board-request at bioinformatics.org
To: bio_bulletin_board at bioinformatics.org
Sent: Mon, 21 Feb 2005 12:34:21 -0500 (EST)
Subject: BiO_Bulletin_Board Digest, Vol 4, Issue 8
> ------------------------------
>
> Message: 3
> Date: Fri, 18 Feb 2005 15:13:20 +0100
> From: Yannick Wurm
> Subject: [BiO BB] Refined Blast?
> To: bio_bulletin_board at bioinformatics.org
> Message-ID: <3E591300-81B7-11D9-A931-000D93712582 at unil.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
> for a specific need in my lab, we are looking for an implementation of
> nucleotide sequence alignment program which would be more flexible than
> standard BLAST.
> The reason is that we have sequenced dna fragments which have been
> submitted to chemical modifications which differentially affects
> different nucleotides.
>
> To help identify these sequences, we need to be able to fine-tune the
> matrix used for scoring. Thus, for example when calculating the "score"
> of an aligment, C->A and C->T could be given different weights.
>
> According to ebi.ac.uk, the WU-blast matrix is:
> A T G C
> A 5
> T -4 5
> G -4 -4 5
> C -4 -4 -4 5
>
> We want to be able to specifiy inidividual values to something like the
> following example:
> A T G C
> A 2
> T -4 8
> G -8 -10 3
> C -2 -1 -3 10
>
> To my surprise, BLAST does not have this liberty, despite the fact that
> different scoring matrices are used for proteins. I couldn't find
> anything on Google either.
>
> Would anyone one the list have a clue? Or do I need to get dirty
> messing with BLAST's source?
> Thanks in advance,
>
> Yannick
>
> . . . . . . . . . . . . . . . . . .
> yannick.wurm at unil.ch
> +41.21.692.4157
> PhD student, Departement of Ecology and Evolution
> Universit? de Lausanne, Switzerland
>
From idh at poulet.org Wed Feb 23 03:25:18 2005
From: idh at poulet.org (Yannick Wurm)
Date: Wed, 23 Feb 2005 09:25:18 +0100
Subject: [BiO BB] Fwd: [blast-help] Refined nucleotide BLAST matrix
Message-ID: <74ba7e5b39c948f2fc204aca2c7a402c@poulet.org>
And so this is the reference Peter mentioned, as kindly indicated by
Wayne Matten at NCBI.
@article{States1991Improved-Sensit,
Abstract = {Scoring matrices for nucleic acid sequence comparison that
are based on models appropriate to the analysis of molecular sequencing
errors or biological mutation processes are presented. In mammalian
genomes, transition mutations occur significantly more frequently than
transversions, and the optimal scoring of sequence alignments based on
this substitution model differs from that derived assuming a uniform
mutation model. The information from sequence alignments potentially
available using an optimal scoring system is compared with that
obtained using the BLASTN default scoring. A modified BLAST database
search tool allows these, or other explicitly specified scoring
matrices, to be utilized in computationally efficient queries of
nucleic acid databases with nucleic acid query sequences. Results of
searches performed using BLASTN's default score matrix are compared
with those using scores based on a mutational model in which
transitions are more prevalent than transversions.},
Author = {David J. States and Warren Gish and Stephen F. Altschul},
Date-Added = {2005-02-23 09:14:28 +0100},
Date-Modified = {2005-02-23 09:15:41 +0100},
Journal = {METHODS: A Companion to Methods in Enzymology},
Url = {http://blast.wustl.edu/doc/ntmats.pdf},
Month = {August},
Number = {1},
Pages = {66-70},
Title = {Improved Sensitivity of Nucleic Acid Database Searches Using
Application-Specific Scoring Matrices},
Volume = {3},
Year = {1991}}
Thanks again!
-yannick
Begin forwarded message:
> From: "Matten, Wayne (NIH/NLM)"
> Date: 22 f?vrier 2005 21:23:29 GMT+01:00
> To: 'Yannick Wurm' ,
> "'blast-help at ncbi.nlm.nih.gov'"
> Subject: RE: [blast-help] Refined nucleotide BLAST matrix
>
> Hello,
> ?
> I believe the reference that Peter mentions is this one:
> ?
> http://blast.wustl.edu/doc/ntmats.pdf
> ?
> Peter summed up the "hack" very well. You might need other commandline
> options; turning off the low complexity filter comes to mind.?But you
> can get blastp, within blastall, to run as long as you format the
> database as a protein database and use a matrix name already in the
> /data directory.?You might also get some ideas from here:
> ?
> ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/
> ?
> e.g., NUC4.4.
> ?
>
> Best regards,
> Wayne
>
> <><><><>>><>>>>><><>>><>
> Wayne Matten
> NCBI User Services
. . . . . . . . . . . . . . . . . .
yannick.wurm at unil.ch
+41.21.692.4157
PhD student, Departement of Ecology and Evolution
Universit? de Lausanne, Switzerland
From hjm at tacgi.com Fri Feb 25 16:23:40 2005
From: hjm at tacgi.com (Harry Mangalam)
Date: Fri, 25 Feb 2005 13:23:40 -0800
Subject: [BiO BB] tacg ver 4.1 now at sourceforge
In-Reply-To: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
References: <20050220052826.66428.qmail@web61102.mail.yahoo.com>
Message-ID: <200502251323.40295.hjm@tacgi.com>
People have been bugging me to release recent work on tacg and while
I've been happy to oblige on a case by case basis, I haven't update
the sourceforge release for a (very long) while. Now I have.
tacg is a GPL'ed command-line program for *nix that performs many of
the common routines in pattern matching in biological strings. It was
originally designed for restriction enzyme analysis and while that
still forms a core of the program, it has been expanded to fill more
roles, sort of a 'grep' for DNA.
Like grep, it's relatively small, fast (5-30x comparable GCG apps),
memory efficient (>10x more efficient than the EMBOSS apps), has tons
of options, but has relatively crude text output (except for the PDF
plasmid maps).
See http://tacg.sourceforge.net for details.
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm at tacgi.com
<>