From whatifwhatnext at on.aibn.com  Wed May  1 08:00:02 2002
From: whatifwhatnext at on.aibn.com (Howard Oliver)
Date: Wed, 1 May 2002 08:00:02 -0400
Subject: [BiO BB] Question about Tool for Information Extraction
In-Reply-To: <3CC752EB.9090106@ucalgary.ca>
Message-ID: <LPBBJFBOOBIHPAFBCGCAMEJCOHAA.whatifwhatnext@on.aibn.com>



Hi All:


I have come across a company that is offering a product that automatically
and efficiently extracts information like protein-protein interactions,
post-translational modifications, pathway data from large datasets like
published literature (Over 11 Million abstracts). Their claim is that with
their tool you can quickly find:
?	Find all interacting proteins from literature  and literature and online
dbases
?	Extract the exact type of interaction
?	Visualize the interaction using our Interaction Viewer
?	Move seamlessly between interaction data and abstracts containing them
?	Build network of proteins using our Pathway Builder
?	Gather contextual  information related to the interactions,
i.e. Cellular location, Experimental conditions etc.


Question: Is this and attractive offer that has some novelty?

Would appreciate the feedback.


Howard Oliver
Principal
What If What Next (TM) Consulting
holiver at whatifwhatnext.com
Tel: 416-638-8582
Mobile: 416-432-2764
www.whatifwhatnext.com
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From bio100 at rediffmail.com  Thu May  2 00:42:48 2002
From: bio100 at rediffmail.com (rajeshwar  gongalla)
Date: 2 May 2002 04:42:48 -0000
Subject: [BiO BB] HMM and Metabolic pathway
Message-ID: <20020502044248.30448.qmail@webmail14.rediffmail.com>

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From danag at bioinformatics.weizmann.ac.il  Thu May  2 05:51:20 2002
From: danag at bioinformatics.weizmann.ac.il (Dana)
Date: Thu, 02 May 2002 11:51:20 +0200
Subject: [BiO BB] Question about Tool for Information Extraction
Message-ID: <200205020850.LAA19398@bioinformatics.weizmann.ac.il>

Hi,

It's seems nice product, depending on your needs. However, you should ask
them about the database. If their database is based only on yeast two -
hybrid analysis it could include not accurate data.  I heard about several 
companies and academic research groups that have similar databases.

Cheers,
Dana
_____________ 
Dana Reichmann
email: danag at bioinfo.weizmann.ac.il
http://bioinfo.weizmann.ac.il/~danag


----------
>From: "Howard Oliver" <whatifwhatnext at on.aibn.com>
>To: <bio_bulletin_board at bioinformatics.org>
>Subject: [BiO BB] Question about Tool for Information Extraction
>Date: Wed, May 1, 2002, 2:00 PM
>

>
>
>Hi All:
>
>
>I have come across a company that is offering a product that automatically
>and efficiently extracts information like protein-protein interactions,
>post-translational modifications, pathway data from large datasets like
>published literature (Over 11 Million abstracts). Their claim is that with
>their tool you can quickly find:
>? Find all interacting proteins from literature  and literature and online
>dbases
>? Extract the exact type of interaction
>? Visualize the interaction using our Interaction Viewer
>? Move seamlessly between interaction data and abstracts containing them
>? Build network of proteins using our Pathway Builder
>? Gather contextual  information related to the interactions,
>i.e. Cellular location, Experimental conditions etc.
>
>
>Question: Is this and attractive offer that has some novelty?
>
>Would appreciate the feedback.
>
>
>Howard Oliver
>Principal
>What If What Next (TM) Consulting
>holiver at whatifwhatnext.com
>Tel: 416-638-8582
>Mobile: 416-432-2764
>www.whatifwhatnext.com
>


From paolo at ist.unige.it  Fri May  3 16:20:40 2002
From: paolo at ist.unige.it (Paolo Romano)
Date: Fri, 3 May 2002 22:20:40 +0200 (DFT)
Subject: [BiO BB] NETTAB Call extension
Message-ID: <200205032020.WAA29568@ist.unige.it>

Dear all,

I'm sending this final call to many mailing lists, sorry for
duplications.

Paolo Romano
---
Dear all,

since we received some requests, we decided to extend the
NETTAB and BIXMAS call for papers (software agents and 
bioinformatics) for a few days.
So, if you are interested in submitting a contribution as an
oral communication, please send me a short note including
an abstract and submit the paper within a few days.

Email the abstract to info at nettab.org and submit the paper
at http://www.nettab.org/PR002/ .

Please remember that the deadline for posters is May 31, 2002.

Best regards. Paolo Romano
---
Paolo Romano (paolo.romano at istge.it)
National Cancer Research Institute
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295


From raju2002 at lycos.com  Sat May  4 03:46:59 2002
From: raju2002 at lycos.com (Rajendren Sundaraganapathy)
Date: Sat, 04 May 2002 00:46:59 -0700
Subject: [BiO BB] HMM and Metabolic pathway
Message-ID: <MJNBAOGDAHKLJCAA@mailcity.com>

Hi All,

I have also interested to receive the details about the below subject.

Thanks & regards,

S. Rajendran.
India.

On 2 May 2002 04:42:48 -0000  
 rajeshwar  gongalla wrote:
>Hi,
>    can any body sujjest how HMM(Hidden Markov models) are use ful 
>to find metabolic pathway.First of whether it applicable to 
>metabolic pathways,since HMM are used for linear problems like 
>protein sequences,speach recogination etc.,.Please sujjest me some 
>solution.If any body has any material please mail me to 
>bio100 at rediffmail.com
>
>with regards,
>G.RAJESHWAR
>_________________________________________________________
>Click below to visit monsterindia.com and review jobs in India or 
>Abroad
>http://monsterindia.rediff.com/jobs
>
>_______________________________________________
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
>http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>




From raju2002 at lycos.com  Sat May  4 03:46:59 2002
From: raju2002 at lycos.com (Rajendren Sundaraganapathy)
Date: Sat, 04 May 2002 00:46:59 -0700
Subject: [BiO BB] HMM and Metabolic pathway
Message-ID: <MJNBAOGDAHKLJCAA@mailcity.com>

Hi All,

I have also interested to receive the details about the below subject.

Thanks & regards,

S. Rajendran.
India.

On 2 May 2002 04:42:48 -0000  
 rajeshwar  gongalla wrote:
>Hi,
>    can any body sujjest how HMM(Hidden Markov models) are use ful 
>to find metabolic pathway.First of whether it applicable to 
>metabolic pathways,since HMM are used for linear problems like 
>protein sequences,speach recogination etc.,.Please sujjest me some 
>solution.If any body has any material please mail me to 
>bio100 at rediffmail.com
>
>with regards,
>G.RAJESHWAR
>_________________________________________________________
>Click below to visit monsterindia.com and review jobs in India or 
>Abroad
>http://monsterindia.rediff.com/jobs
>
>_______________________________________________
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
>http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>




From starmachina at hotmail.com  Tue May  7 22:35:43 2002
From: starmachina at hotmail.com (Star Machina)
Date: Tue, 07 May 2002 19:35:43 -0700
Subject: [BiO BB] HELP! Desperate for help with a basic Perl program...
Message-ID: <F177rtRua7ostVvdXuG0000d9d8@hotmail.com>

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From raju2002 at lycos.com  Wed May  8 10:19:05 2002
From: raju2002 at lycos.com (Rajendren Sundaraganapathy)
Date: Wed, 08 May 2002 07:19:05 -0700
Subject: [BiO BB] Reg. HMM
Message-ID: <PIKJPBLCBCKALCAA@mailcity.com>

Hi All,

If anybody knows about HMM (to find out protein family) then please let me know.

Thanks & regards,

Raju.




From sebas at math.umass.edu  Wed May  8 09:39:12 2002
From: sebas at math.umass.edu (Paola Sebastiani)
Date: Wed, 8 May 2002 09:39:12 -0400
Subject: [BiO BB] Methods in functional genomics
Message-ID: <007801c1f695$bd2d57f0$0201000a@sebaslt>

MACHINE LEARNING JOURNAL
Special Issue: Methods in Functional Genomics

This is a remind that the deadline for submitting the abstract is May
15. Abstracts should be sent by email to Paola Sebastiani
(sebas at math.umass.edu).

Details of the special issue are posted at

http://www.genomethods.org/mlj/

Best wishes

Paola

------------------------------------------------------------------
Paola Sebastiani
Assistant Professor
Department of Mathematics and Statistics
University of Massachusetts, 
Amherst, MA, 01003

Telephone: (413)  545-0622
Fax: (413) 545-1801 
email: sebas at math.umass.edu
url:http://www.math.umass.edu/~sebas



From dfield at ceh.ac.uk  Fri May 10 09:50:14 2002
From: dfield at ceh.ac.uk (Dawn Field)
Date: Fri, 10 May 2002 14:50:14 +0100
Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and ecology
Message-ID: <scdbde5f.064@wpo.nerc.ac.uk>

Dear List,

We recently hired a superb research programmer following a post he made to this list about wanting to move from staight IT into bioinformatics  - so we're making sure to post here for this UK studentship.  For more information about the bioinformatics/genomics aspects of the below studentship please feel free to contact me.


ANNOUNCEMENT
A 3-year NERC funded studentship is available for doctoral research,
starting 1st October 2002, to work on the ecology and functional genomics of plasmids, 
supervised by Professor Mark Bailey, Professor John Fry, and Dr. Dawn Field. 

We are seeking a motivated student able to work at the interface of genomics, 
bioinformatics, evolutionary and ecological genetics, and microbial adaptation to develop 
new approaches and methods of addressing key questions about the role of plasmids 
in short and long-term ecological adaptation.  

To apply, please send a CV and details of two referees (name, address, fax,
and email) to Professor Mark Baily, Microbial Ecology Section, CEH Oxford,
Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK residents.

The closing date for applications is the 31st May 2002.


PROJECT BACKGROUND AND DESCRIPTION
Ecological and functional genomic studies to determine the evolutionary contribution 
of plasmids to the horizontal gene pool of bacteria

The revolution in genomics has already produced 60 + published bacterial genome 
sequences and over 230 plasmid sequences for comparison and study.  The study 
of bacterial genome sequences combined with the introduction of large-scale population 
studies of DNA sequence-level variation has led to a paradigm shift in our thinking about 
how fluid bacterial chromosomes are and the amounts of recombination they are able to 
undergo.  An extremely important aspect of this fluid gene pool that has received far 
less attention is the contribution of plasmids, extrachromosomal genetic elements that 
persist and replicate independently of the host genome.  The significance of 
understanding this horizontal gene pool (HGP) lies in attempting to understand how, 
when and why plasmids contribute to the evolution fitness, persistence, and ecological 
role of a given host in a specific environment.

For the last decade we have studied the microbial genetics of plant associated 
pseudomonads and demonstrated the direct co-operation between host and plasmid 
in local adaptation to the niche.  Current questions we are trying to address include: 
How does plasmid host-range evolve? What selective pressures control plasmid 
persistence or extinction in populations? How different/similar is the genome structure 
and gene content of plasmids taken from the same host? Which plasmid genes/sequences 
are responsible for specific host phenotypes and adaptation? Do rates of recombination 
differ within plasmids when compared to their host chromosome?  To answer these broad 
questions, we need to collect, analyse, and integrate information obtained from a variety 
of experimental and computer-based approaches including:  1) population-level and 
phylogenetic studies of genetic variation found in plasmid and host populations, 2) comparative 
genomics analysis of plasmids and their hosts, 3) transcriptomic studies of plasmid genes 
expressed only in certain hosts/environments, and 4) proteomic studies of host-specific 
and environment-specific protein profiles collected using state-of-the-art proteomic 
technologies.

Students with undergraduate or MRes degrees (or significant research experience) in 
the fields of Ecology, Evolution, Microbiology, or Computational biology (Bioinformatics)
are strongly encouraged to apply.  Students with a background in Computer Science, 
Maths, Statistics, or a related field with a strong desire to learn biological principles will 
also be considered.  The student will be located in the Laboratories of Mark Bailey 
(mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford and be registered 
for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the University of Cardiff.







From msalisbury at genomeweb.com  Fri May 10 11:33:54 2002
From: msalisbury at genomeweb.com (Meredith Salisbury)
Date: Fri, 10 May 2002 11:33:54 -0400
Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and ecology
In-Reply-To: <scdbde5f.064@wpo.nerc.ac.uk>
Message-ID: <NDBBIJAHNLHKEHDFPJGBGEOKEAAA.msalisbury@genomeweb.com>

Hi Dawn,

I'm with Genome Technology magazine and saw your recent post.  I'm working
on an article about what kind of training people need for bioinformatics and
what positions they should look for or expect, and was wondering if I could
talk to you for some information about what the hiring side is looking for.

Thanks so much,
Meredith


___________________
Meredith Salisbury
Managing Editor, Genome Technology
+1.212.651.5635



> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Dawn
> Field
> Sent: Friday, May 10, 2002 9:50 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and
> ecology
>
>
> Dear List,
>
> We recently hired a superb research programmer following a post
> he made to this list about wanting to move from staight IT into
> bioinformatics  - so we're making sure to post here for this UK
> studentship.  For more information about the
> bioinformatics/genomics aspects of the below studentship please
> feel free to contact me.
>
>
> ANNOUNCEMENT
> A 3-year NERC funded studentship is available for doctoral research,
> starting 1st October 2002, to work on the ecology and functional
> genomics of plasmids,
> supervised by Professor Mark Bailey, Professor John Fry, and Dr.
> Dawn Field.
>
> We are seeking a motivated student able to work at the interface
> of genomics,
> bioinformatics, evolutionary and ecological genetics, and
> microbial adaptation to develop
> new approaches and methods of addressing key questions about the
> role of plasmids
> in short and long-term ecological adaptation.
>
> To apply, please send a CV and details of two referees (name,
> address, fax,
> and email) to Professor Mark Baily, Microbial Ecology Section, CEH Oxford,
> Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK residents.
>
> The closing date for applications is the 31st May 2002.
>
>
> PROJECT BACKGROUND AND DESCRIPTION
> Ecological and functional genomic studies to determine the
> evolutionary contribution
> of plasmids to the horizontal gene pool of bacteria
>
> The revolution in genomics has already produced 60 + published
> bacterial genome
> sequences and over 230 plasmid sequences for comparison and
> study.  The study
> of bacterial genome sequences combined with the introduction of
> large-scale population
> studies of DNA sequence-level variation has led to a paradigm
> shift in our thinking about
> how fluid bacterial chromosomes are and the amounts of
> recombination they are able to
> undergo.  An extremely important aspect of this fluid gene pool
> that has received far
> less attention is the contribution of plasmids, extrachromosomal
> genetic elements that
> persist and replicate independently of the host genome.  The
> significance of
> understanding this horizontal gene pool (HGP) lies in attempting
> to understand how,
> when and why plasmids contribute to the evolution fitness,
> persistence, and ecological
> role of a given host in a specific environment.
>
> For the last decade we have studied the microbial genetics of
> plant associated
> pseudomonads and demonstrated the direct co-operation between
> host and plasmid
> in local adaptation to the niche.  Current questions we are
> trying to address include:
> How does plasmid host-range evolve? What selective pressures
> control plasmid
> persistence or extinction in populations? How different/similar
> is the genome structure
> and gene content of plasmids taken from the same host? Which
> plasmid genes/sequences
> are responsible for specific host phenotypes and adaptation? Do
> rates of recombination
> differ within plasmids when compared to their host chromosome?
> To answer these broad
> questions, we need to collect, analyse, and integrate information
> obtained from a variety
> of experimental and computer-based approaches including:  1)
> population-level and
> phylogenetic studies of genetic variation found in plasmid and
> host populations, 2) comparative
> genomics analysis of plasmids and their hosts, 3) transcriptomic
> studies of plasmid genes
> expressed only in certain hosts/environments, and 4) proteomic
> studies of host-specific
> and environment-specific protein profiles collected using
> state-of-the-art proteomic
> technologies.
>
> Students with undergraduate or MRes degrees (or significant
> research experience) in
> the fields of Ecology, Evolution, Microbiology, or Computational
> biology (Bioinformatics)
> are strongly encouraged to apply.  Students with a background in
> Computer Science,
> Maths, Statistics, or a related field with a strong desire to
> learn biological principles will
> also be considered.  The student will be located in the
> Laboratories of Mark Bailey
> (mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford
> and be registered
> for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the
> University of Cardiff.
>
>
>
>
>
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>




From jay at charterglobal.com  Fri May 10 10:10:19 2002
From: jay at charterglobal.com (Jay N Swamy)
Date: Fri, 10 May 2002 10:10:19 -0400
Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and ecology
In-Reply-To: <NDBBIJAHNLHKEHDFPJGBGEOKEAAA.msalisbury@genomeweb.com>
Message-ID: <NFBBIBLKILLABHMCIKPLEEPLFBAA.jay@charterglobal.com>

Hi Meredith, Dawn,

I work with an IT Consulting firm with a specialized focus on serving
pharmaceutical companies. A number of our employees are keen on getting
trained and moving into the area of Bioinformatics. It would be a great help
if you could let us know what sort of training these IT professionals need
to undertake and also if you know of any Institutes, bodies or Universities
offering programs towards this end.

Thanks & Regards,

Jay

-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of
Meredith Salisbury
Sent: Friday, May 10, 2002 11:34 AM
To: bio_bulletin_board at bioinformatics.org
Subject: RE: [BiO BB] PhD post in plasmid bioinformatics, genomics and
ecology


Hi Dawn,

I'm with Genome Technology magazine and saw your recent post.  I'm working
on an article about what kind of training people need for bioinformatics and
what positions they should look for or expect, and was wondering if I could
talk to you for some information about what the hiring side is looking for.

Thanks so much,
Meredith


___________________
Meredith Salisbury
Managing Editor, Genome Technology
+1.212.651.5635



> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Dawn
> Field
> Sent: Friday, May 10, 2002 9:50 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and
> ecology
>
>
> Dear List,
>
> We recently hired a superb research programmer following a post
> he made to this list about wanting to move from staight IT into
> bioinformatics  - so we're making sure to post here for this UK
> studentship.  For more information about the
> bioinformatics/genomics aspects of the below studentship please
> feel free to contact me.
>
>
> ANNOUNCEMENT
> A 3-year NERC funded studentship is available for doctoral research,
> starting 1st October 2002, to work on the ecology and functional
> genomics of plasmids,
> supervised by Professor Mark Bailey, Professor John Fry, and Dr.
> Dawn Field.
>
> We are seeking a motivated student able to work at the interface
> of genomics,
> bioinformatics, evolutionary and ecological genetics, and
> microbial adaptation to develop
> new approaches and methods of addressing key questions about the
> role of plasmids
> in short and long-term ecological adaptation.
>
> To apply, please send a CV and details of two referees (name,
> address, fax,
> and email) to Professor Mark Baily, Microbial Ecology Section, CEH Oxford,
> Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK residents.
>
> The closing date for applications is the 31st May 2002.
>
>
> PROJECT BACKGROUND AND DESCRIPTION
> Ecological and functional genomic studies to determine the
> evolutionary contribution
> of plasmids to the horizontal gene pool of bacteria
>
> The revolution in genomics has already produced 60 + published
> bacterial genome
> sequences and over 230 plasmid sequences for comparison and
> study.  The study
> of bacterial genome sequences combined with the introduction of
> large-scale population
> studies of DNA sequence-level variation has led to a paradigm
> shift in our thinking about
> how fluid bacterial chromosomes are and the amounts of
> recombination they are able to
> undergo.  An extremely important aspect of this fluid gene pool
> that has received far
> less attention is the contribution of plasmids, extrachromosomal
> genetic elements that
> persist and replicate independently of the host genome.  The
> significance of
> understanding this horizontal gene pool (HGP) lies in attempting
> to understand how,
> when and why plasmids contribute to the evolution fitness,
> persistence, and ecological
> role of a given host in a specific environment.
>
> For the last decade we have studied the microbial genetics of
> plant associated
> pseudomonads and demonstrated the direct co-operation between
> host and plasmid
> in local adaptation to the niche.  Current questions we are
> trying to address include:
> How does plasmid host-range evolve? What selective pressures
> control plasmid
> persistence or extinction in populations? How different/similar
> is the genome structure
> and gene content of plasmids taken from the same host? Which
> plasmid genes/sequences
> are responsible for specific host phenotypes and adaptation? Do
> rates of recombination
> differ within plasmids when compared to their host chromosome?
> To answer these broad
> questions, we need to collect, analyse, and integrate information
> obtained from a variety
> of experimental and computer-based approaches including:  1)
> population-level and
> phylogenetic studies of genetic variation found in plasmid and
> host populations, 2) comparative
> genomics analysis of plasmids and their hosts, 3) transcriptomic
> studies of plasmid genes
> expressed only in certain hosts/environments, and 4) proteomic
> studies of host-specific
> and environment-specific protein profiles collected using
> state-of-the-art proteomic
> technologies.
>
> Students with undergraduate or MRes degrees (or significant
> research experience) in
> the fields of Ecology, Evolution, Microbiology, or Computational
> biology (Bioinformatics)
> are strongly encouraged to apply.  Students with a background in
> Computer Science,
> Maths, Statistics, or a related field with a strong desire to
> learn biological principles will
> also be considered.  The student will be located in the
> Laboratories of Mark Bailey
> (mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford
> and be registered
> for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the
> University of Cardiff.
>
>
>
>
>
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>


_______________________________________________
BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
http://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From pac at bcm.tmc.edu  Fri May 10 14:18:35 2002
From: pac at bcm.tmc.edu (Pam Culpepper)
Date: Fri, 10 May 2002 13:18:35 -0500
Subject: [BiO BB] I've Been Having Problems
Message-ID: <CBENJPLNNJINGHDBEMDDEEAJCAAA.pac@bcm.tmc.edu>

Someone asked me if I would share my script for downloading Genbank files on
a daily basis.

I've been having horrendous problems with MS products of all kinds.  I had
to reformat and rebuild
my hard drive due to the dreaded registry problems.  I am a Unix/Mac/Linux
person and I think my MS office
system knows this.

At any rate, I lost all my mail.

I don't have a script to download Genbank files on a daily basis.  If you
want Genbank records, I suggest
you download the ASN1 files and then do an asn2gb (in the toolkit/demo
directory) for the Genbank records.
asn2ff (also in the toolkit/demo directory) will output Fasta-formatted
sequences which you would then fmerge with your Blast databases.

If you're interested in a script that would do this, I can put one together
for you.

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

In response to the "What training to you need for Bioinformatics?" let me
say that when I started in bioinformatics I had no bioinformatics
background, just a solid computing/mathematical/engineering background.  I
picked up the biology by reading Genes V, Biological Sequence Analysis,
Biostatistics, etc. and working with sequence analysis tools.

Pam



From velazquezcat at hotmail.com  Fri May 10 19:04:40 2002
From: velazquezcat at hotmail.com (Catherine Velazquez)
Date: Fri, 10 May 2002 16:04:40 -0700
Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and ecology
Message-ID: <F213dlUz0j4oyjRedjO00011716@hotmail.com>

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From pallabi2k at yahoo.com  Mon May 13 03:31:06 2002
From: pallabi2k at yahoo.com (pallavi sarmah)
Date: Mon, 13 May 2002 00:31:06 -0700 (PDT)
Subject: [BiO BB] (no subject)
Message-ID: <20020513073106.38995.qmail@web12004.mail.yahoo.com>


Respected Sir

I am an Agricultural graduate presently pursuing a P.G Diploma course in Bioinformatics from Amity Institute of Biotechnology, Can you please suggest the prospect and the companies recruiting graduates with a diploma .

Thanking you

Pallavi Sarmah



---------------------------------
Do You Yahoo!?
LAUNCH - Your Yahoo! Music Experience
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From jkwaran at rediffmail.com  Tue May 14 05:02:47 2002
From: jkwaran at rediffmail.com (j  kamesh)
Date: 14 May 2002 09:02:47 -0000
Subject: [BiO BB] (no subject)
Message-ID: <20020514090247.32464.qmail@webmail14.rediffmail.com>

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From jay at charterglobal.com  Tue May 14 07:46:06 2002
From: jay at charterglobal.com (Jay N Swamy)
Date: Tue, 14 May 2002 07:46:06 -0400
Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and ecology
In-Reply-To: <F213dlUz0j4oyjRedjO00011716@hotmail.com>
Message-ID: <NFBBIBLKILLABHMCIKPLGEANFCAA.jay@charterglobal.com>

Thanks Cat..that is a big help!!

Jay
  -----Original Message-----
  From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Catherine
Velazquez
  Sent: Friday, May 10, 2002 7:05 PM
  To: bio_bulletin_board at bioinformatics.org
  Subject: RE: [BiO BB] PhD post in plasmid bioinformatics, genomics and
ecology


  Jay,

  I know there are courses in both bioinformatics programming and use of
bioinformatic-esque databases at both San Jose State University www.sjsu.edu
and Cal State Hayward.

  The University of California, Santa Cruz has a B.S. degree in
Bioinformatics that started in Fall '00.  www.ucsc.edu

  People can register as Open University students, Post-Bacc students or
enroll in the 2nd degree program.



  Toodles,

  Cat






  Check out these nifty concert pictures!!
  >From: "Jay N Swamy"
  >Reply-To: bio_bulletin_board at bioinformatics.org
  >To:
  >Subject: RE: [BiO BB] PhD post in plasmid bioinformatics, genomics and
ecology
  >Date: Fri, 10 May 2002 10:10:19 -0400
  >
  >Hi Meredith, Dawn,
  >
  >I work with an IT Consulting firm with a specialized focus on serving
  >pharmaceutical companies. A number of our employees are keen on getting
  >trained and moving into the area of Bioinformatics. It would be a great
help
  >if you could let us know what sort of training these IT professionals
need
  >to undertake and also if you know of any Institutes, bodies or
Universities
  >offering programs towards this end.
  >
  >Thanks & Regards,
  >
  >Jay
  >
  >-----Original Message-----
  >From: bio_bulletin_board-admin at bioinformatics.org
  >[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of
  >Meredith Salisbury
  >Sent: Friday, May 10, 2002 11:34 AM
  >To: bio_bulletin_board at bioinformatics.org
  >Subject: RE: [BiO BB] PhD post in plasmid bioinformatics, genomics and
  >ecology
  >
  >
  >Hi Dawn,
  >
  >I'm with Genome Technology magazine and saw your recent post. I'm working
  >on an article about what kind of training people need for bioinformatics
and
  >what positions they should look for or expect, and was wondering if I
could
  >talk to you for some information about what the hiring side is looking
for.
  >
  >Thanks so much,
  >Meredith
  >
  >
  >___________________
  >Meredith Salisbury
  >Managing Editor, Genome Technology
  >+1.212.651.5635
  >
  >
  >
  > > -----Original Message-----
  > > From: bio_bulletin_board-admin at bioinformatics.org
  > > [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Dawn
  > > Field
  > > Sent: Friday, May 10, 2002 9:50 AM
  > > To: bio_bulletin_board at bioinformatics.org
  > > Subject: [BiO BB] PhD post in plasmid bioinformatics, genomics and
  > > ecology
  > >
  > >
  > > Dear List,
  > >
  > > We recently hired a superb research programmer following a post
  > > he made to this list about wanting to move from staight IT into
  > > bioinformatics - so we're making sure to post here for this UK
  > > studentship. For more information about the
  > > bioinformatics/genomics aspects of the below studentship please
  > > feel free to contact me.
  > >
  > >
  > > ANNOUNCEMENT
  > > A 3-year NERC funded studentship is available for doctoral research,
  > > starting 1st October 2002, to work on the ecology and functional
  > > genomics of plasmids,
  > > supervised by Professor Mark Bailey, Professor John Fry, and Dr.
  > > Dawn Field.
  > >
  > > We are seeking a motivated student able to work at the interface
  > > of genomics,
  > > bioinformatics, evolutionary and ecological genetics, and
  > > microbial adaptation to develop
  > > new approaches and methods of addressing key questions about the
  > > role of plasmids
  > > in short and long-term ecological adaptation.
  > >
  > > To apply, please send a CV and details of two referees (name,
  > > address, fax,
  > > and email) to Professor Mark Baily, Microbial Ecology Section, CEH
Oxford,
  > > Mansfield Rd, Oxford OX1 3SR. Applications are invited from UK
residents.
  > >
  > > The closing date for applications is the 31st May 2002.
  > >
  > >
  > > PROJECT BACKGROUND AND DESCRIPTION
  > > Ecological and functional genomic studies to determine the
  > > evolutionary contribution
  > > of plasmids to the horizontal gene pool of bacteria
  > >
  > > The revolution in genomics has already produced 60 + published
  > > bacterial genome
  > > sequences and over 230 plasmid sequences for comparison and
  > > study. The study
  > > of bacterial genome sequences combined with the introduction of
  > > large-scale population
  > > studies of DNA sequence-level variation has led to a paradigm
  > > shift in our thinking about
  > > how fluid bacterial chromosomes are and the amounts of
  > > recombination they are able to
  > > undergo. An extremely important aspect of this fluid gene pool
  > > that has received far
  > > less attention is the contribution of plasmids, extrachromosomal
  > > genetic elements that
  > > persist and replicate independently of the host genome. The
  > > significance of
  > > understanding this horizontal gene pool (HGP) lies in attempting
  > > to understand how,
  > > when and why plasmids contribute to the evolution fitness,
  > > persistence, and ecological
  > > role of a given host in a specific environment.
  > >
  > > For the last decade we have studied the microbial genetics of
  > > plant associated
  > > pseudomonads and demonstrated the direct co-operation between
  > > host and plasmid
  > > in local adaptation to the niche. Current questions we are
  > > trying to address include:
  > > How does plasmid host-range evolve? What selective pressures
  > > control plasmid
  > > persistence or extinction in populations? How different/similar
  > > is the genome structure
  > > and gene content of plasmids taken from the same host? Which
  > > plasmid genes/sequences
  > > are responsible for specific host phenotypes and adaptation? Do
  > > rates of recombination
  > > differ within plasmids when compared to their host chromosome?
  > > To answer these broad
  > > questions, we need to collect, analyse, and integrate information
  > > obtained from a variety
  > > of experimental and computer-based approaches including: 1)
  > > population-level and
  > > phylogenetic studies of genetic variation found in plasmid and
  > > host populations, 2) comparative
  > > genomics analysis of plasmids and their hosts, 3) transcriptomic
  > > studies of plasmid genes
  > > expressed only in certain hosts/environments, and 4) proteomic
  > > studies of host-specific
  > > and environment-specific protein profiles collected using
  > > state-of-the-art proteomic
  > > technologies.
  > >
  > > Students with undergraduate or MRes degrees (or significant
  > > research experience) in
  > > the fields of Ecology, Evolution, Microbiology, or Computational
  > > biology (Bioinformatics)
  > > are strongly encouraged to apply. Students with a background in
  > > Computer Science,
  > > Maths, Statistics, or a related field with a strong desire to
  > > learn biological principles will
  > > also be considered. The student will be located in the
  > > Laboratories of Mark Bailey
  > > (mbj at ceh.ac.uk) and Dawn Field (Dfield at ceh.ac.uk) at CEH-Oxford
  > > and be registered
  > > for a NERC funded PhD with John Fry (fry at cardiff.ac.uk) at the
  > > University of Cardiff.
  > >
  > >
  > >
  > >
  > >
  > > _______________________________________________
  > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
  > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
  > >
  >
  >
  >_______________________________________________
  >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
  >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
  >
  >_______________________________________________
  >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
  >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board


----------------------------------------------------------------------------
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From mucastic at yahoo.com  Tue May 14 13:57:24 2002
From: mucastic at yahoo.com (Harini Kumar)
Date: Tue, 14 May 2002 10:57:24 -0700 (PDT)
Subject: [BiO BB] masters in bioinformatics
In-Reply-To: <20020513073106.38995.qmail@web12004.mail.yahoo.com>
Message-ID: <20020514175724.54623.qmail@web13806.mail.yahoo.com>

To whomsoever who can HELP me!
I am an "almost" graduate student in electronics and
comm. engg.I have always been interested in genomics
and biotechnology.
I'd like to do a masters in Bioinformatics.It would be
helpful if someome out thr could give me ANY
information abt the various univs,school(public or
private) offering this course.
Further,I'd like to know if thr are any pre-requisite
subjects that I should have covered at the bachelor's
level in order to pursue a masters in Bioinformatics.
thanks,
H. 

__________________________________________________
Do You Yahoo!?
LAUNCH - Your Yahoo! Music Experience
http://launch.yahoo.com


From jeff at bioinformatics.org  Tue May 14 14:13:58 2002
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Tue, 14 May 2002 14:13:58 -0400
Subject: [BiO BB] FAQ (was: masters in bioinformatics)
References: <20020514175724.54623.qmail@web13806.mail.yahoo.com>
Message-ID: <3CE153E6.A6E49679@bioinformatics.org>

Anyone wanting to know about education in bioinformatics (prerequisites,
courses, programs, schools) should check out our FAQ:

  http://bioinformatics.org/faq/

It's written by Damian Counsell and contributed to by more than 30 other
people, I bet the most extensive general bioinformatics FAQ on the planet.

Cheers.
Jeff

Harini Kumar wrote:
> 
> To whomsoever who can HELP me!
> I am an "almost" graduate student in electronics and
> comm. engg.I have always been interested in genomics
> and biotechnology.
> I'd like to do a masters in Bioinformatics.It would be
> helpful if someome out thr could give me ANY
> information abt the various univs,school(public or
> private) offering this course.
> Further,I'd like to know if thr are any pre-requisite
> subjects that I should have covered at the bachelor's
> level in order to pursue a masters in Bioinformatics.
> thanks,
> H.

-- 
J.W. Bizzaro                                jeff at bioinformatics.org
Director, Bioinformatics.Org        http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                   -- Benjamin Franklin
--


From rouellette at umuc.edu  Tue May 14 14:22:08 2002
From: rouellette at umuc.edu (Robert Ouellette)
Date: Tue, 14 May 2002 14:22:08 -0400
Subject: [BiO BB] masters in bioinformatics
References: <20020514175724.54623.qmail@web13806.mail.yahoo.com>
Message-ID: <3CE155D0.BA4C8BBC@umuc.edu>

UMUC plan to offer a track in Bioinformatics Practice as part of the
current Biotechnology studies program in the fall 2002.  All clasess are
available online via the Internet
bob

Harini Kumar wrote:

> To whomsoever who can HELP me!
> I am an "almost" graduate student in electronics and
> comm. engg.I have always been interested in genomics
> and biotechnology.
> I'd like to do a masters in Bioinformatics.It would be
> helpful if someome out thr could give me ANY
> information abt the various univs,school(public or
> private) offering this course.
> Further,I'd like to know if thr are any pre-requisite
> subjects that I should have covered at the bachelor's
> level in order to pursue a masters in Bioinformatics.
> thanks,
> H.
>
> __________________________________________________
> Do You Yahoo!?
> LAUNCH - Your Yahoo! Music Experience
> http://launch.yahoo.com
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board



From velazquezcat at hotmail.com  Tue May 14 21:26:52 2002
From: velazquezcat at hotmail.com (Catherine Velazquez)
Date: Tue, 14 May 2002 18:26:52 -0700
Subject: [BiO BB] masters in bioinformatics
Message-ID: <F273sl3xbYiMCIqtQvA0000eee3@hotmail.com>

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From hello_sushil2k at yahoo.com  Wed May 15 10:05:03 2002
From: hello_sushil2k at yahoo.com (sushil kumar)
Date: Wed, 15 May 2002 07:05:03 -0700 (PDT)
Subject: [BiO BB] about job-prospect
Message-ID: <20020515140503.57011.qmail@web14005.mail.yahoo.com>

Respected sir;

i'm  a chemistry graduate and currently doing Post
Graduate course(1 1/2yrs) course at Institute of
Bioinformatics and Applied Biotechnology(IBAB) ,ITPL
Banglore.This is the first batch of this
institute.This institute has state of art lab facility
and  well experienced faculties from IISc and
NCBS.Faculties from industries like Biocon
group,Monsanto,Strand genomics,Astrazeneca are coming
to train us.what are the possiblities for me(as a
chemistry graduate)? in your institution?
yours' 
sushil kumar singh
IBAB
Banglore

__________________________________________________
Do You Yahoo!?
LAUNCH - Your Yahoo! Music Experience
http://launch.yahoo.com


From ogd116 at mail.usask.ca  Thu May 16 08:42:49 2002
From: ogd116 at mail.usask.ca (Ognen Duzlevski)
Date: 16 May 2002 06:42:49 -0600
Subject: [BiO BB] internship ooportunities in bioinformatics
Message-ID: <1021552973.2592.97.camel@aquaos.myip.org>

Hello,

I am a comp sci student in Canada commencing my final year of undergrad
studies and have decided to take some bioinformatics courses offered at
our University so that my degree is officially with a track in
bioinformatics. In the meantime I am looking for an internship in the
United States, mostly for gaining real-world experience in the field
(money is really not a serious requirement - I would work for less as
long as its a fun and learning experience). I have worked and been
associated for more than one year with the National Research Council of
Canada's Plant Biotechnology Institute where I have developed a
multi-threaded version of clustalw available for free download in source
code form from http://bioinfo.pbi.nrc.ca/clustalw-smp/ (application note
pending review with the Journal of Bioinformatics) and I realized I
rather enjoy optimizing/parallelizing old and producing new
bioinformatics applications.

If anyone has an idea of where to look for an internship, please let me
know. I have 2+ years work experience (working full-time while being an
undergrad) and have been programming for the past 10+ years as a hobby.

Thank you,
Ognen Duzlevski
--
Saskatoon, SK, Canada



From somak_ray at yahoo.com  Thu May 16 17:15:52 2002
From: somak_ray at yahoo.com (Somak Ray)
Date: Thu, 16 May 2002 14:15:52 -0700 (PDT)
Subject: [BiO BB] M.S courses in bioinformatics
Message-ID: <20020516211552.56763.qmail@web11607.mail.yahoo.com>

For M.S and other courses in bioinformatics  follow
this link:

http://123genomics.homestead.com/files/courses.html

Regards

Somak Ray

__________________________________________________
Do You Yahoo!?
LAUNCH - Your Yahoo! Music Experience
http://launch.yahoo.com


From ejournalist at hotmail.com  Fri May 17 09:36:37 2002
From: ejournalist at hotmail.com (Caroline Talbot-crosdale)
Date: Fri, 17 May 2002 09:36:37 -0400
Subject: [BiO BB] (no subject)
Message-ID: <F155siHOiij5QZDFMMe00016419@hotmail.com>

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From sjayu20 at yahoo.com  Fri May 24 04:37:49 2002
From: sjayu20 at yahoo.com (Jay)
Date: Fri, 24 May 2002 01:37:49 -0700 (PDT)
Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #257 - 3 msgs
In-Reply-To: <200205141601.g4EG1ZE19048@www.bioinformatics.org>
Message-ID: <20020524083749.24097.qmail@web11301.mail.yahoo.com>


Hi,

 

Can anyone tell me if there are any bioinfomatics (shoret term and long term) courses available in Chennai . 

 

Thanks & Regards


Jay


---------------------------------
Do You Yahoo!?
LAUNCH - Your Yahoo! Music Experience
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From manan_atit at yahoo.com  Fri May 24 12:12:54 2002
From: manan_atit at yahoo.com (Manan Atit)
Date: Fri, 24 May 2002 11:12:54 -0500
Subject: [BiO BB] Bioinformatics in Houston
In-Reply-To: <200205241601.g4OG1XE23447@www.bioinformatics.org>
Message-ID: <003201c2033d$e06f3cb0$6501a8c0@monkey>

Are there any bioinformatics resources or courses in Houston?

Regards,
Manan






From sravan_111 at rediffmail.com  Mon May 27 09:50:26 2002
From: sravan_111 at rediffmail.com (sravan  sravan)
Date: 27 May 2002 13:50:26 -0000
Subject: [BiO BB] (no subject)
Message-ID: <20020527135026.3302.qmail@webmail10.rediffmail.com>

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From merc99 at indiatimes.com  Tue May 28 03:07:10 2002
From: merc99 at indiatimes.com (merc99)
Date: Tue, 28 May 2002 12:37:10 +0530
Subject: [BiO BB] newcomer
Message-ID: <200205280700.MAA21668@WS0005.indiatimes.com>

hi!


I am a new comer in this field. can anyone tell me how to go about it. anything would be helpful. thanks


merc
Get Your Private, Free E-mail from Indiatimes at  http://email.indiatimes.com
Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in
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From paolo at ist.unige.it  Tue May 28 06:44:39 2002
From: paolo at ist.unige.it (Paolo Romano)
Date: Tue, 28 May 2002 12:44:39 +0200 (DFT)
Subject: [BiO BB] CFP: NETTAB 2002 Agents in Bioinformatics
Message-ID: <200205281044.MAA15874@ist.unige.it>

Dear colleagues,

this is the final remind for the poster submission deadline
for the NETTAB 2002 Workshop on "Agents in Bioinformatics"
that will be held in Bologna, Italy, from July 12 to 14, 2002.

Workshop site available at: http://www.nettab.org/2002/
Scientific Programme: http://www.nettab.org/2002/progr.html
Call for papers: http://www.nettab.org/2002/call.html
Abstract submission form: http://www.nettab.org/PR2002/submit.html

The same deadline applies to the early registration fees.
You are therefore invited to subscribe to the NETTAB Workshop
before next friday May 31, 2002.

I hope to see many of you in Bologna.

Best regards. Paolo Romano
-- 
Paolo Romano (paolo.romano at istge.it)
National Cancer Research Institute
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295



From Joel.Dudley at asu.edu  Tue May 28 13:17:28 2002
From: Joel.Dudley at asu.edu (Joel Dudley)
Date: Tue, 28 May 2002 10:17:28 -0700
Subject: [BiO BB] newcomer
Message-ID: <7D2FB294FA311F4299D03CC8D390437071651C@mainex5.asu.edu>

If you told us your background it may be easier to offer some advice. 
 
Joel Dudley 
Faculty Research Associate 
Arizona State University 
Kumar Laboratory of Evolutionary Functional Genomics 
http://lsweb.la.asu.edu/skumar/ <http://lsweb.la.asu.edu/skumar/>  

-----Original Message-----
From: merc99 [mailto:merc99 at indiatimes.com]
Sent: Tuesday, May 28, 2002 12:07 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] newcomer



hi!

I am a new comer in this field. can anyone tell me how to go about it.
anything would be helpful. thanks

merc

  _____  

Get Your Private, Free E-mail from Indiatimes at
<http://email.indiatimes.com> http://email.indiatimes.com
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From dbeach at email.unc.edu  Tue May 28 14:56:30 2002
From: dbeach at email.unc.edu (Dale Beach)
Date: Tue, 28 May 2002 14:56:30 -0400
Subject: [BiO BB] Web Based Sequence Manipulations
Message-ID: <367404870.1022597790@spindle.bio.unc.edu>

Hey Folks-

I am hoping that your collective brains can help me find a web based 
software suite to do some simple DNA sequence manipulations.  Basically I'd 
like to find "Strider" on the web.

I'll be teaching a "Molecular Biology for Science Wirters" class in two 
weeks.  We will complete the class by cloning and sequenceing a gene, and 
we would like to do some sequence analysis with the students.  Simply 
looking at the sequence, translation, rev/comp sorts of things.  However, 
we don't really want to install software on all of the classroom computers. 
(OK the computer support people gave us a hard time last year.)  The 
software should be quick and easy so that we can lead them through the 
analysis quickly as a group.

Feel free to reply to my email address directly so that this doesn't 
clutter the list.

Thanks in advance for any helpful URLs!
dale

PS- If you mention Pedro's Tools, please specify useful (read "not Dead") 
links.

Dale Beach
622 Fordham Hall CB3280
University of North Carolina
Chapel Hill, NC 27599-3280

Voice- (919) 962-2363
FAX  - (919) 962-8461
dbeach at email.unc.edu


From gary at www.bioinformatics.org  Tue May 28 16:20:27 2002
From: gary at www.bioinformatics.org (Gary Van Domselaar)
Date: Tue, 28 May 2002 16:20:27 -0400 (EDT)
Subject: [BiO BB] Web Based Sequence Manipulations
In-Reply-To: <367404870.1022597790@spindle.bio.unc.edu>
Message-ID: <Pine.LNX.4.33.0205281611530.31361-100000@www.bioinformatics.org>

On Tue, 28 May 2002, Dale Beach wrote:

> Hey Folks-
>
> I am hoping that your collective brains can help me find a web based
> software suite to do some simple DNA sequence manipulations.  Basically I'd
> like to find "Strider" on the web.

Bioinformatics.Org hosts SMS (Sequence Manipulation Suite) by Paul
Stothard.  Check out

http://bioinformatics.org/sms/

It has over 35 separate programs for DNA and protein manipulation.  It  is
an excellent (and free) suite of programs written in Javascript, so there
is not installation required, yet all the processing is done client-side
so it is quick.  All the forms have example inputs as defaults, so its
easy to understand and use.  It sounds like a perfect fit for your
requirements.


Regards,

Gary Van Domselaar

gary at bioinformatics.org





>
> I'll be teaching a "Molecular Biology for Science Wirters" class in two
> weeks.  We will complete the class by cloning and sequenceing a gene, and
> we would like to do some sequence analysis with the students.  Simply
> looking at the sequence, translation, rev/comp sorts of things.  However,
> we don't really want to install software on all of the classroom computers.
> (OK the computer support people gave us a hard time last year.)  The
> software should be quick and easy so that we can lead them through the
> analysis quickly as a group.
>
> Feel free to reply to my email address directly so that this doesn't
> clutter the list.
>
> Thanks in advance for any helpful URLs!
> dale
>
> PS- If you mention Pedro's Tools, please specify useful (read "not Dead")
> links.
>
> Dale Beach
> 622 Fordham Hall CB3280
> University of North Carolina
> Chapel Hill, NC 27599-3280
>
> Voice- (919) 962-2363
> FAX  - (919) 962-8461
> dbeach at email.unc.edu
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>



From gigya74 at hotmail.com  Wed May 29 02:39:01 2002
From: gigya74 at hotmail.com (girish)
Date: Wed, 29 May 2002 12:09:01 +0530 (India Standard Time)
Subject: [BiO BB] in search of new job
Message-ID: <3CF47785.000003.57417@bgts20.bgts.co.in>

hi all
i am venkataraman. i am a software programmer with 2 yrs experience. i am
also an msc in biotech from baroda. i would like to know if any company is
recruting people. shall pass on more info later.
thanking you
venkataraman
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From vijayendran_vijay at hotmail.com  Wed May 29 05:57:01 2002
From: vijayendran_vijay at hotmail.com (vijay endran)
Date: Wed, 29 May 2002 09:57:01 +0000
Subject: [BiO BB] docking
Message-ID: <F123cOvJOugA9VnvMAT0000b396@hotmail.com>


hello everyone,

i am intrested in protein-ligand docking studies,for this i have used GRAMM 
software.
But when i use this software the ligand shape changes !
if any one of you who have already worked in it, can get me a solution to 
avoid this.

thanking you.

c.vijayendran.

_________________________________________________________________
Join the world?s largest e-mail service with MSN Hotmail. 
http://www.hotmail.com



From oxp108 at psu.edu  Wed May 29 13:50:42 2002
From: oxp108 at psu.edu (Helen Piontkivska)
Date: Wed, 29 May 2002 13:50:42 -0400
Subject: [BiO BB] Web Based Sequence Manipulations
Message-ID: <17576.020529@psu.edu>

Hi Dale,

here are two sites to consider:
1) Baylor College hosts a great collection of web-based tools for
sequence analysis - http://searchlauncher.bcm.tmc.edu/
2) EBI tools http://www.ebi.ac.uk/Tools/sequence.html

Cheers,
Helen
________________________________________________

Helen Piontkivska
Institute of Molecular Evolutionary Genetics and
Department of Biology
208 Mueller Lab
Pennsylvania State University
University Park, PA 16802
Tel: 1(814)8657030
Email: oxp108 at psu.edu
http://www.bio.psu.edu/People/Gradstud/Piontkiv/
________________________________________________




From raju2002 at lycos.com  Thu May 30 01:07:56 2002
From: raju2002 at lycos.com (Raju S)
Date: Wed, 29 May 2002 22:07:56 -0700
Subject: [BiO BB] in search of new job
Message-ID: <ONIAIAGKOKMKBDAA@mailcity.com>

Hi Venkataraman,

Please forward your resume to my email address. If your resume suits our requirement then I will revert back to you.

Regards,

S. Raju
raju2002 at lycos.com

-----------------------------
On Wed, 29 May 2002 12:09:01  
 girish wrote:
>hi all

>i am venkataraman. i am a software programmer with 2 yrs experience. i am
>also an msc in biotech from baroda. i would like to know if any company is
>recruting people. shall pass on more info later.

>thanking you

>venkataraman


________________________________________________________
Outgrown your current e-mail service?
Get a 25MB Inbox, POP3 Access, No Ads and No Taglines with LYCOS MAIL PLUS.
http://login.mail.lycos.com/brandPage.shtml?pageId=plus


From praveen at sysarris.soft.net  Tue May 28 10:12:26 2002
From: praveen at sysarris.soft.net (Praveen)
Date: Tue, 28 May 2002 19:42:26 +0530
Subject: [BiO BB] hi
Message-ID: <000c01c20651$b2e67300$4f66a8c0@praveen>

Hi,

we are on look for Biotech (Life Science) profile, preferably with
Microbiology background with Genomic and Proteomics background. The location
is Bangalore.

The role could be some one like a product manager to study and come out with
a vision
for software products in the areas of Genomic and Proteomics.
Experience in pre-sales & post-sales support is desirable (helping marketing
staff).
Able to make presentations for prospects.
Will decide on scope of product, interact with the development team,
research on competitive products, collect info from prospect/customer
discussions.
Will be a member of the bioinfo team.
Should be an IT Literate and flair towards business development

we have requirement for 3 to 4 candidates, incase you have any reference
within your contact circles please refer them to me.




Best Wishes

Praveen
SysArris Software
Bangalore-India
Tel. No. 91-80-6654965,6655052,6642690
Fax No. 91-80-6650374
http://www.sysarris.com/




From danag at bioinformatics.weizmann.ac.il  Thu May 30 10:17:17 2002
From: danag at bioinformatics.weizmann.ac.il (Dana Reichmann)
Date: Thu, 30 May 2002 17:17:17 +0300
Subject: [BiO BB] correlation mutation database
Message-ID: <B91C0F1D.89%danag@bioinfo.weizmann.ac.il>

Hello,

I am working on development a tool for correlation mutation prediction  in
complex of two proteins.
I am looking for database of correlated mutation in protein complexes.  Does
anyone familiar with such database?
I will be happy to get any help on this subject, such as known algorithms
and programs for checking correlation mutation in structure and sequences.

Thanks a lot,
Dana





From whatifwhatnext at on.aibn.com  Thu May 30 14:57:10 2002
From: whatifwhatnext at on.aibn.com (Howard Oliver)
Date: Thu, 30 May 2002 14:57:10 -0400
Subject: [BiO BB] hi
In-Reply-To: <000c01c20651$b2e67300$4f66a8c0@praveen>
Message-ID: <LPBBJFBOOBIHPAFBCGCAOENMOIAA.whatifwhatnext@on.aibn.com>

Hi Praveen;

I would be very interested in this work. I have a deep understanding of the
proteomics sector. Please take a look at our website which contains the
following offer. I look forward to further interaction

Regards;


Howard Oliver
Principal
What If What Next (TM) Consulting
holiver at whatifwhatnext.com
Tel: 416-638-8582
Mobile: 416-432-2764
www.whatifwhatnext.com:

>>>>>>>><<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>
>>>>>>>>>>

An Open Proposal for a Proteomics/Bioinformatics Business Development
Project

It is a common practice for senior management to seek new ideas and third
party input into internally generated strategic and tactical planning. With
our domain knowledge and unique approach to scenario charting and business
development, we can be a cost effective source of such intelligence. For
focus, we can explore the development of your business by creating an
alternate Trade RouteTM Strategy.

The work can begin with a Scenario Charting exercise. Scenario Charting is
most effective when focused on a strategically important question - for
example:

 Can alliance partners innovatively integrate old and new technologies to
gain market share from exclusively ?denovo? innovation in emerging vertical
markets?


We would bring to this discussion our research and experience in Proteomics
and Bioinformatics, and network of contacts in the field. We bring
particular value to issues related to the convergence of Biotechnology and
IT.

Deliverable: A detailed six month Business Development Action Plan
containing strategy and specifications for near term opportunities. The
document would detail:

 Market intelligence and alternative strategic insights

 Near term opportunities including new vertical markets and possible
alliances

 Areas for enhancement and integration of existing science and technology

 Alternatives for tuning overall value propositions and business cases

 Detailed resource requirements


A  clear leap up the Omic evolutionary ladder! If this is of interest for
your organization, contact Howard Oliver directly at 416-638-8582 or
holiver at whatifwhatnext.com .

>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>



-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Praveen
Sent: Tuesday, May 28, 2002 10:12 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] hi


Hi,

we are on look for Biotech (Life Science) profile, preferably with
Microbiology background with Genomic and Proteomics background. The location
is Bangalore.

The role could be some one like a product manager to study and come out with
a vision
for software products in the areas of Genomic and Proteomics.
Experience in pre-sales & post-sales support is desirable (helping marketing
staff).
Able to make presentations for prospects.
Will decide on scope of product, interact with the development team,
research on competitive products, collect info from prospect/customer
discussions.
Will be a member of the bioinfo team.
Should be an IT Literate and flair towards business development

we have requirement for 3 to 4 candidates, incase you have any reference
within your contact circles please refer them to me.




Best Wishes

Praveen
SysArris Software
Bangalore-India
Tel. No. 91-80-6654965,6655052,6642690
Fax No. 91-80-6650374
http://www.sysarris.com/


_______________________________________________
BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
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From wdstein at vms.huji.ac.il  Fri May 31 07:03:08 2002
From: wdstein at vms.huji.ac.il (Wilfred D. Stein)
Date: Fri, 31 May 2002 13:03:08 +0200
Subject: [BiO BB] AC numbers
Message-ID: <3.0.1.32.20020531130308.01427b0c@vms.huji.ac.il>

I am using a paper which has GenBank accession numbers in the form
AC003080, for instance.  How do I find the relevant sequnce from
GenBank..GenBank does NOT accept such AC or AL numbers

wds


Yours sincerely,
Wilfred D. Stein
(Emeritus Professor of Biophysics)

BIOLOGICAL CHEMISTRY
SILBERMAN INSTITUTE OF LIFE SCIENCES
HEBREW UNIVERSITY of  JERUSALEM
GIVAT RAM, JERUSALEM 91904 ISRAEL
Tel + (+972) 2 6585679 (office)   6525649 (home)
Cellular phone : (+972) 51 822391
Fax :   (+972) 2 6585440
Email : WDSTEIN at HUJI.AC.IL




From Neeraj_Tripathi at satyam.com  Fri May 31 07:35:40 2002
From: Neeraj_Tripathi at satyam.com (Neeraj_Tripathi)
Date: Fri, 31 May 2002 17:05:40 +0530
Subject: [BiO BB] AC numbers
Message-ID: <877B003B6F03D511A22E00B0D078E7A80ADE7B2C@hst.satyam.com>

Hi Wilfred, 
   Please go to NCBI site (http://www.ncbi.nlm.nih.gov/entrez) and choose
"Nucleotide" as database. Submit the AC number and you get the URL for the
accession number. Go to the URL, change the 'Display' as "FASTA" in the
drop-down box and you get the sequence in FASTA format.

rgds
Neeraj

> ----------
> From: 	Wilfred D. Stein[SMTP:wdstein at vms.huji.ac.il]
> Reply To: 	bio_bulletin_board at bioinformatics.org
> Sent: 	Friday, May 31, 2002 4:33 PM
> To: 	bio_bulletin_board at bioinformatics.org
> Subject: 	[BiO BB] AC numbers
> 
> I am using a paper which has GenBank accession numbers in the form
> AC003080, for instance.  How do I find the relevant sequnce from
> GenBank..GenBank does NOT accept such AC or AL numbers
> 
> wds
> 
> 
> Yours sincerely,
> Wilfred D. Stein
> (Emeritus Professor of Biophysics)
> 
> BIOLOGICAL CHEMISTRY
> SILBERMAN INSTITUTE OF LIFE SCIENCES
> HEBREW UNIVERSITY of  JERUSALEM
> GIVAT RAM, JERUSALEM 91904 ISRAEL
> Tel + (+972) 2 6585679 (office)   6525649 (home)
> Cellular phone : (+972) 51 822391
> Fax :   (+972) 2 6585440
> Email : WDSTEIN at HUJI.AC.IL
> 
> 
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
************************************************************************** 
This email (including any attachments) is intended for the sole use of the
intended recipient/s and may contain material that is CONFIDENTIAL AND
PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or
distribution or forwarding of any or all of the contents in this message is
STRICTLY PROHIBITED. If you are not the intended recipient, please contact
the sender by email and delete all copies; your cooperation in this regard
is appreciated.
**************************************************************************


From subba.raju at hbh.ilabsgroup.com  Fri May 31 06:46:27 2002
From: subba.raju at hbh.ilabsgroup.com (Subba.Raju)
Date: Fri, 31 May 2002 16:16:27 +0530
Subject: [BiO BB] AC numbers
Message-ID: <759BC7ED1B0BD6118BC400B0D0E16A1F5A8A6B@BHILLS3NT002>

hi,
did u really tried the NCBI's Genbank - entrez interface.
it should support accession numbers. in fact the acccession u have given
will retrieve sequence of gi|2588627.

just log on top the site and specify the accession no in the nucleotide
option query box of entrez
ok

cheers
Subba

-----Original Message-----
From: Wilfred D. Stein [mailto:wdstein at vms.huji.ac.il]
Sent: Friday, May 31, 2002 4:33 PM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] AC numbers


I am using a paper which has GenBank accession numbers in the form
AC003080, for instance.  How do I find the relevant sequnce from
GenBank..GenBank does NOT accept such AC or AL numbers

wds


Yours sincerely,
Wilfred D. Stein
(Emeritus Professor of Biophysics)

BIOLOGICAL CHEMISTRY
SILBERMAN INSTITUTE OF LIFE SCIENCES
HEBREW UNIVERSITY of  JERUSALEM
GIVAT RAM, JERUSALEM 91904 ISRAEL
Tel + (+972) 2 6585679 (office)   6525649 (home)
Cellular phone : (+972) 51 822391
Fax :   (+972) 2 6585440
Email : WDSTEIN at HUJI.AC.IL


_______________________________________________
BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
http://bioinformatics.org/mailman/listinfo/bio_bulletin_board


From A.Bossers at id.dlo.nl  Fri May 31 06:43:34 2002
From: A.Bossers at id.dlo.nl (Bossers, A.)
Date: Fri, 31 May 2002 12:43:34 +0200
Subject: [BiO BB] AC numbers
Message-ID: <EA56C399C5A6D5118B5400508BF98376475ABF@id008s.id.dlo.nl>

Wilfred,

use a Sequence retrievel system like:
http://www.cmbi.kun.nl/srs6/

Start a session, select all nt databases and do quicksearch AC003080.


Gives you the hit:
http://www.cmbi.kun.nl/srs6bin/cgi-bin/wgetz?-id+5YRLe1IsMix+-e+[EMBL:'AC003
080']


Good luck~!

@lex




> -----Original Message-----
> From: Wilfred D. Stein [mailto:wdstein at vms.huji.ac.il]
> Sent: Friday, May 31, 2002 1:03 PM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] AC numbers
> 
> 
> I am using a paper which has GenBank accession numbers in the form
> AC003080, for instance.  How do I find the relevant sequnce from
> GenBank..GenBank does NOT accept such AC or AL numbers
> 
> wds
> 
> 
> Yours sincerely,
> Wilfred D. Stein
> (Emeritus Professor of Biophysics)
> 
> BIOLOGICAL CHEMISTRY
> SILBERMAN INSTITUTE OF LIFE SCIENCES
> HEBREW UNIVERSITY of  JERUSALEM
> GIVAT RAM, JERUSALEM 91904 ISRAEL
> Tel + (+972) 2 6585679 (office)   6525649 (home)
> Cellular phone : (+972) 51 822391
> Fax :   (+972) 2 6585440
> Email : WDSTEIN at HUJI.AC.IL
> 
> 
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 


From amosfolarin78 at hotmail.com  Fri May 31 08:51:23 2002
From: amosfolarin78 at hotmail.com (amos folarin)
Date: Fri, 31 May 2002 12:51:23 +0000
Subject: [BiO BB] Information on Profiles
Message-ID: <F252ym2aaHYqAFqF2620000a8a7@hotmail.com>

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From msch at soi.city.ac.uk  Fri May 31 09:10:41 2002
From: msch at soi.city.ac.uk (Michael Schroeder)
Date: Fri, 31 May 2002 14:10:41 +0100 (BST)
Subject: [BiO BB] 2 Research Fellow/Assistant posts at City University, London
Message-ID: <Pine.GSO.4.05.10205311320450.9058-100000@altair.soi.city.ac.uk>

			     GeneStream:
	 Massive Genetic Data will become Critical Knowledge


		  2 Research Fellow/Assistant posts

				  at

	 Department of Computing, City University, London, UK



Post 1: Salary: 19,760 to 24,656 pa inclusive London Allowance
Post 2: Salary: 32,953 pa inclusive London Allowance
Fixed term for 12 months
Closing date: 20 June 2002

GeneStream is   a  1.5M European   project involving partners  in  the
Netherlands, Germany,  UK,   Poland, France, Cyprus,  and  Greece. The
purpose  of GeneStream is to  achieve  a technological breakthrough in
the  automatic categorisation   and structuring  of  large volumes  of
biological  data. Developments in  this  project  are targeted  at the
organisation,   classification,    management,  and   distribution  of
unstructured information. The  information originates from both within
an organisation and external  sources     and is available  in    many
different formats including  experimental data, target  identification
data, lead  discovery, pharmaceutical and toxicological data, clinical
data,  patient      filling data. The     data    is  unstructured  or
semi-structured and accessible  online,  through databases, or  legacy
systems. It is available in text, HTML, or XML.

GeneStream will produce insights into   the best method for   managing
timely  and accurate  supply of mission   critical information in  the
biotechnology sector, thus turning unstructured data into knowledge.

The postholders   will be responsible for  carrying  out  research and
development to build a platform to categories and integrate biological
information.  The postholders will be  expected  to have  a degree  in
Computer Science, Engineering, or   Bioinformatics: and PhD   in these
areas is essential  for the more senior of  the two posts.  Candidates
need good software  development skills including experience with  Java
and XML. Scientifically, the candidates  have to show excellence in at
least   one   of  the  following  areas:  bioinformatics,  information
retrieval     technology,  ontologies,   agent  technology, databases,
information visualisation.

This is an excellent opportunity  to gain experience in  international
collaborative research and development. The successful candidates will
have regular meetings with the international project partners and will
have  the opportunity to present results  to partners and at workshops
and conferences. Commercial exploitation  of the project's results are
an integral part of the project.

The postholders will  be part of   the expanding, currently  15 people
strong  agents  group  at City  University's Department  of Computing,
which   has  been rated    4B    in the recent    research  assessment
exercise. City University is located  in "City-side", a thriving  area
with many restaurants, theatres, and pubs. The Department of Computing
is located in University's newly refurbished Innovation Centre.

We are committed to  equal opportunities.  For further particulars and
an application   form visit  www.city.ac.uk/hr/jobs or  alternatively,
send a large (A4) stamped (41p) addressed envelope to Karen Hutson, HR
Department, City   University, Northampton Square,  London,  EC1V 0HB,
detailing your name address and   post reference number: KH6853.   For
informal      enquiries    please      email    Michael      Schroeder
(msch at soi.city.ac.uk).  Deaf  people can reach  us through the minicom
on 020 7040 8931.

Closing date: 20 June 2002

http://www.city.ac.uk



---
Dr. Michael Schroeder
Department of Computing
School of Informatics, City University
Northampton Square, London, EC1V 0HB, UK
Room: CIC208
t: ++44 20 7040 8918
f: ++44 20 7040 8587
e: msch at soi.city.ac.uk
w: http://www.soi.city.ac.uk/~msch/