[Biodevelopers] Gene classification

Tue Jul 29 13:53:45 EDT 2003

Hi all,

I am not sure if this question reached the group though I mailed it earlier.
I wish to know what the industry standard for gene classification (into
exons and introns) is.  This is to be able to compare my results with an
industry standard benchmark.

(I apologize if this message has been duplicated).

Thanks,

Srivatsan Pallavaram
Image Processing Research Lab [IPRL] (Prof. Sanjit K Mitra - group)
Dept. of Electrical and Computer Engineering
University of California, Santa Barbara
---
----- Original Message ----- 
From: <biodevelopers-request at bioinformatics.org>
To: <biodevelopers at bioinformatics.org>
Sent: Tuesday, July 29, 2003 9:02 AM
Subject: Biodevelopers digest, Vol 1 #145 - 3 msgs

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>    1. XML schema/API for BLAST? (Fangxia Li)
>    2. Re: Biodevelopers digest, Vol 1 #144 - 2 msgs (Allen Henry)
>    3. Re: XML schema/API for BLAST? (Mitchell Skinner)
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> --__--__--
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> Message: 1
> Date: Mon, 28 Jul 2003 10:58:46 -0700 (PDT)
> From: Fangxia Li <fangxia_li at yahoo.com>
> To: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] XML schema/API for BLAST?
> Reply-To: biodevelopers at bioinformatics.org
>
> Dear all,
>
> Anyone knows if BLAST support XML API and where I can
> find the XML schema for BLAST search. Anyone got some
> sample codes (including search input and output in XML
> format)
>
> Regards,
> Scott
>
> Bioinformatics Developer
> Thomas Jefferson University
> Philadelphia, PA 19107
>
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> Message: 2
> Date: Mon, 28 Jul 2003 15:02:44 -0700 (PDT)
> From: Allen Henry <allen_777 at yahoo.com>
> To: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #144 - 2 msgs
> Reply-To: biodevelopers at bioinformatics.org
>
> I think the code for the Rosetta algo is available on
> SourceForge, but do not know if it is parallelized.
>
> Hope this helps
>
>
> --- biodevelopers-request at bioinformatics.org wrote:
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> >    1. rosetta (Jaroslaw Zola)
> >    2. Re: Gen DNA sequences (ledaval at ibb.unesp.br)
> >
> > -- __--__-- 
> >
> > Message: 1
> > Date: Mon, 28 Jul 2003 13:05:49 +0200 (CEST)
> > From: Jaroslaw Zola <zola at icis.pcz.czest.pl>
> > To: Biodevelopers <biodevelopers at bioinformatics.org>
> > Subject: [Biodevelopers] rosetta
> > Reply-To: biodevelopers at bioinformatics.org
> >
> > Hi - I'm looking for some good papers on Rosetta
> > Algorithm. Does anybody
> > know if there exists parallel implementation of
> > Rosetta?
> >
> > Regards,
> >
> > j.zola
> >
> > --
> >
>
=2E........................................................................=
> > =2E..
> > Jaros=B3aw =AFola=09=09      Instytut Informatyki
> > Teoretycznej i Stosowanej
> > tel/fax: (034) 3250589=09                =09
> > Politechnika Cz=EAstochowska
> > zola at icis.pcz.czest.pl=09=09=09 D=B1browskiego 73,
> > 42-200 Cz=EAstochowa
> >
>
=2E........................................................................=
> > =2E..
> >
> >
> > -- __--__-- 
> >
> > Message: 2
> > Date: Mon, 28 Jul 2003 12:44:55 -0300 (BRT)
> > Subject: Re: [Biodevelopers] Gen DNA sequences
> > From: <ledaval at ibb.unesp.br>
> > To: <biodevelopers at bioinformatics.org>
> > Reply-To: biodevelopers at bioinformatics.org
> >
> > HI,
> > if you go to nucleotide at NCBI and put the name of
> > the genes you are
> > interested in you will find the sequences of these
> > genes with introns and
> > exons to the majority of them. You can also enter in
> > Sanger
> > (http://www.sanger.ac.uk). You will find usefull
> > information there too.
> >
> > Leda Isabel de Castro Valente Esteves
> > PhD student
> > Genetics Department
> > IBB - UNESP
> > Brazil
> >
> > > Hello,
> > >
> > > I'm a PhD student at Valencia, Spain. I'm working
> > in pattern
> > > recognition techniques applied to bioinformatic.
> > >
> > > I'm searching at SRS and NCBI pairs of genes
> > sequences and their
> > > protein trancripted associated sequences.
> > >
> > > The problem is that I get the mRNA sequences or
> > sequences of a full
> > > chromosome but not a piece of DNA sequeces with
> > the protein associated,
> > > with introns and other subsequences.
> > >
> > > Do you know how to get it or a database with this
> > kind of information?
> > >
> > > Best regards,
> > > Juan Miguel Garcia
> > >
> > >
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> =====
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> =================================================================
>
> Al Henry (408) 799-9404 cell
>
> allen_777 at yahoo.com
>
>
>
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> Message: 3
> Subject: Re: [Biodevelopers] XML schema/API for BLAST?
> From: Mitchell Skinner <mitchskin at comcast.net>
> To: biodevelopers at bioinformatics.org
> Organization:
> Date: 29 Jul 2003 03:32:49 -0700
> Reply-To: biodevelopers at bioinformatics.org
>
> Hello,
>
> NCBI has an XML DTD for its blast output at
> ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NCBI_BlastOutput.dtd
>
> The BLAST XML readme at
> ftp://ftp.ncbi.nlm.nih.gov/blast/documents/README.blxml
> may also be useful.  It contains more description of the blast xml
> output.
>
> If you're asking whether there is an xml-rpc or SOAP interface to the
> blast web service, then I'm not aware of any.  If you're wanting to
> script blast runs, though, then running locally may be easier in any
> case.
>
> HTH,
> Mitch
>
> On Mon, 2003-07-28 at 10:58, Fangxia Li wrote:
> > Dear all,
> >
> > Anyone knows if BLAST support XML API and where I can
> > find the XML schema for BLAST search. Anyone got some
> > sample codes (including search input and output in XML
> > format)
> >
> > Regards,
> > Scott
> >
> > Bioinformatics Developer
> > Thomas Jefferson University
> > Philadelphia, PA 19107
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site design software
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>
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