[Biodevelopers] Re: Biodevelopers digest, Vol 1 #146 - 5 msgs
ramasubbu venkatesh
venky at earthlink.net
Wed Jul 30 12:28:27 EDT 2003
This is in response to "Gene Classification" question by Srivatsan. I am not
sure there is an "Industry standard". But you can talk about canonical
splicing (vs alternative splicing). There is a tool called Spidey at the
NCBI website which identifies exons and introns(by inference). It is well
documented, has a web interface and easy to use. Executable can be
downloaded too. You can benchmark your results against its results.
Hope this helps.
Venky
Ramasubbu Venkatesh, Ph.D.
Bioinformatics Consultant
----- Original Message -----
From: <biodevelopers-request at bioinformatics.org>
To: <biodevelopers at bioinformatics.org>
Sent: Wednesday, July 30, 2003 9:02 AM
Subject: Biodevelopers digest, Vol 1 #146 - 5 msgs
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> Today's Topics:
>
> 1. XML BLAST (Ela Hunt)
> 2. Re: Biodevelopers digest, Vol 1 #145 - 3 msgs (Junwen wang)
> 3. Re: XML schema/API for BLAST? (Abhik Shah)
> 4. Gene classification (Srivatsan Pallavaram)
> 5. Re: XML schema/API for BLAST? (David Huen)
>
> --__--__--
>
> Message: 1
> From: Ela Hunt <ela at dcs.gla.ac.uk>
> To: biodevelopers at bioinformatics.org
> Date: Tue, 29 Jul 2003 17:16:41 +0100
> Cc: Fangxia Li <fangxia_li at yahoo.com>
> Subject: [Biodevelopers] XML BLAST
> Reply-To: biodevelopers at bioinformatics.org
>
> Hi,
> 1. Blast has an output option producing XML, -m 7
>
> -m alignment view options:
> 0 = pairwise,
> 1 = query-anchored showing identities,
> 2 = query-anchored no identities,
> 3 = flat query-anchored, show identities,
> 4 = flat query-anchored, no identities,
> 5 = query-anchored no identities and blunt ends,
> 6 = flat query-anchored, no identities and blunt ends,
> 7 = XML Blast output,
> 8 = tabular [Integer]
> default = 0
>
> 2. I parsed it a while ago using a SAX parser, just to try it out, so my
> software is not robust, but it was easy. I think I had to add a top level
> node to the DTD, so that a bunch of results (each being a separate XML
record
> but all in one file) could be read in as a tree. Possibly robust solutions
> are out there to be found.
> Ela
>
> --
> _________________________________________________________________________
>
> Ela Pustulka-Hunt MA MPhil BA PhD Email: ela at dcs.gla.ac.uk
> MRC Research Fellow Phone: +44 141 330 6034
> Fax: +44 141 330 4913
>
> University of Glasgow, Department of Computing Science,
> 8-17 Lilybank Gardens, Glasgow G12 8QQ, SCOTLAND
> http://www.dcs.gla.ac.uk/~ela
> _________________________________________________________________________
>
> --__--__--
>
> Message: 2
> Date: Tue, 29 Jul 2003 12:53:39 -0400 (EDT)
> From: Junwen wang <junwen at astro.ocis.temple.edu>
> To: fangxia_li at yahoo.com
> Cc: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] Re: Biodevelopers digest, Vol 1 #145 - 3 msgs
> 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
> My experience with BLAST xml output is that it is easier to hard code the
> parser, The XML parser is difficult to use and hard to debug.
>
> Junwen
>
> --__--__--
>
> Message: 3
> Date: Mon, 28 Jul 2003 11:34:00 -0700 (PDT)
> From: Abhik Shah <android5 at hyperreal.org>
> To: biodevelopers at bioinformatics.org
> Subject: Re: [Biodevelopers] XML schema/API for BLAST?
> Reply-To: biodevelopers at bioinformatics.org
>
> I know for sure that NCBI's Blast supports XML output. The XML Schema is
> here:
>
> http://www.kaiseryang.com/bio/db/NCBI_XSD.html
>
> BioPerl, BioJava and others have parsers (and possibly example code) for
> the XML output. As for input, I don't think NCBI's Blast supports XML-RPC
> or SOAP. IBM has some free SOAP wrappers for common bioinformatics
> services (including BLAST) here:
>
> http://www.alphaworks.ibm.com/tech/ws4LS
>
> or you can just write you own wrapper..
>
> Abhik.
> University of Michigan.
>
>
>
>
> On Mon, 28 Jul 2003, 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
> >
> > __________________________________
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> > Biodevelopers at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> >
>
> --__--__--
>
> Message: 4
> From: "Srivatsan Pallavaram" <srivaths at engineering.ucsb.edu>
> To: <biodevelopers at bioinformatics.org>
> Date: Tue, 29 Jul 2003 10:53:45 -0700
> Subject: [Biodevelopers] Gene classification
> Reply-To: biodevelopers at bioinformatics.org
>
> 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
>
>
> > Send Biodevelopers mailing list submissions to
> > biodevelopers at bioinformatics.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> > or, via email, send a message with subject or body 'help' to
> > biodevelopers-request at bioinformatics.org
> >
> > You can reach the person managing the list at
> > biodevelopers-admin at bioinformatics.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Biodevelopers digest..."
> >
> >
> > Today's Topics:
> >
> > 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)
> >
> > -- __--__--
> >
> > 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
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site design software
> > http://sitebuilder.yahoo.com
> >
> > -- __--__--
> >
> > 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:
> > > Send Biodevelopers mailing list submissions to
> > > biodevelopers at bioinformatics.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web,
> > > visit
> > >
> > >
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> > > or, via email, send a message with subject or body
> > > 'help' to
> > > biodevelopers-request at bioinformatics.org
> > >
> > > You can reach the person managing the list at
> > > biodevelopers-admin at bioinformatics.org
> > >
> > > When replying, please edit your Subject line so it
> > > is more specific
> > > than "Re: Contents of Biodevelopers digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 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
> > > >
> > > >
> > > > _______________________________________________
> > > > Biodevelopers mailing list
> > > > Biodevelopers at bioinformatics.org
> > > >
> > >
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> > >
> > >
> > >
> > >
> > >
> > > -- __--__--
> > >
> > > _______________________________________________
> > > Biodevelopers mailing list
> > > Biodevelopers at bioinformatics.org
> > >
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> > >
> > >
> > > End of Biodevelopers Digest
> >
> >
> > =====
> >
> > =================================================================
> >
> > Al Henry (408) 799-9404 cell
> >
> > allen_777 at yahoo.com
> >
> >
> >
> >
> >
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site design software
> > http://sitebuilder.yahoo.com
> >
> > -- __--__--
> >
> > 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
> > > http://sitebuilder.yahoo.com
> > > _______________________________________________
> > > Biodevelopers mailing list
> > > Biodevelopers at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/biodevelopers
> >
> >
> >
> > -- __--__--
> >
> > _______________________________________________
> > Biodevelopers mailing list
> > Biodevelopers at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> >
> >
> > End of Biodevelopers Digest
> >
>
>
> --__--__--
>
> Message: 5
> Date: Tue, 29 Jul 2003 21:45:40 +0100 (BST)
> From: David Huen <smh1008 at cus.cam.ac.uk>
> To: biodevelopers at bioinformatics.org
> Subject: Re: [Biodevelopers] XML schema/API for BLAST?
> Reply-To: biodevelopers at bioinformatics.org
>
> On Mon, 28 Jul 2003, Abhik Shah wrote:
>
> > I know for sure that NCBI's Blast supports XML output. The XML Schema is
> > here:
> >
> > http://www.kaiseryang.com/bio/db/NCBI_XSD.html
> >
> > BioPerl, BioJava and others have parsers (and possibly example code)
for
> > the XML output. As for input, I don't think NCBI's Blast supports
XML-RPC
> > or SOAP. IBM has some free SOAP wrappers for common bioinformatics
> > services (including BLAST) here:
> >
> I don't know about the rest but Biojava has some Blast XML support
> although it needs updating to work with the latest format (i.e. I hear the
> latest doesn't concat the outputs together from multiple queries forming a
> unparsable mess). There is example code in the demos in the package. That
> will be done eventually. However, use of the Biojava parser does require
> some understanding of its parsing framework as the parser parses blast XML
> and generates SAX calls to simulate the parsing of an equivalent file in
> our standard internal XML format. That way, we share a common downstream
> parser framework for all our parsers (Blast/FASTA/etc).
>
> Rgds,
> David Huen
>
>
>
>
> --__--__--
>
> _______________________________________________
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> https://bioinformatics.org/mailman/listinfo/biodevelopers
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>
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