[Biojava-l] How to launch a blast on ncbi server via biojava?
bertrand beckert
bertrand.beckert at gmail.com
Fri Sep 7 11:23:13 UTC 2007
Yes it could be nice...
For the moment, as I said before the biojava blast parser seem to doesn't
work
I made my own EBI result parser by using XMLBeans and the XML schema of the
EBI XML result.
thanks for your help
Bertrand
2007/9/6, Stefan Goetz <sgoetz at cipf.es >:
>
> Hi Bertrand,
> Blast2GO uses the NCBI Qblast to run, retrieve and parse blasts since
> several years and is completly implemted in Java and works stable. Maybe
> you would like to have a look at the aplication first and if you think
> that would suit you or be helpfull we can see if I can "cut out" some
> code.
> Try http://www.blast2go.org/.
> Best regards,
> Stefan
>
>
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org
> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
> > bertrand beckert
> > Sent: Thursday, September 06, 2007 3:21 PM
> > To: Mark Schreiber
> > Cc: biojava-l at lists.open-bio.org; Dickson Guedes
> > Subject: Re: [Biojava-l] How to launch a blast on ncbi server
> > via biojava?
> >
> >
> > Thanks for all those answers
> >
> > So first I tried the NCBI blast interface which you can found at:
> > http://users.encs.concordia.ca/~f_kohant/ncbiblast/<http://users.encs.concordia.ca/%7Ef_kohant/ncbiblast/>
> > which work, but the result are in xhtml format....
> > then I test the EBI webservice for NCBI blast which also work
> > and teh result
> > are in xml format.
> > I use the biojava Blast XML parser, but always some exception occurs:
> > org.xml.sax.SAXException : Could not recognise the format of
> > this file as one
> > supported by the framework
> > at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(
> > BlastLikeSAXParser.java:182)....
> > I also tried to put the parsing in the lazy mode but it doesn't change
> > anything.
> >
> > Remark:
> > the BlastLikeSAXParser seem to be able to parse the NCBI
> > Blast version:
> > 2.0.11 , 2.2.2 , 2.2.3
> > and the blast version received is : program
> > name="NCBI-blastn" version="
> > 2.2.15 "....
> >
> > Bertrand
> >
> >
> > 2007/9/4, Mark Schreiber <markjschreiber at gmail.com >:
> > >
> > > Hi -
> > >
> > > BioJava doesn't have a mechanism to do this however EBI
> > does expose a
> > > webservice for NCBI BLAST. The details can be found at
> > > http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast
> > >
> > > They have a java client with source code you could reuse.
> > >
> > > You can then use biojava to parse the results. If the results are in
> > > XML you can use biojava's BLAST XML parser or you could
> > just use XPath
> > > to get the bits you want.
> > >
> > > If you build a solution that makes use of biojava it would
> > be great if
> > > you can add it to the cookbook section of the biojava wiki.
> > >
> > > - Mark
> > >
> > > On 9/4/07, bertrand beckert <bertrand.beckert at gmail.com> wrote:
> > > > Thanks for this code...
> > > > but this piece is good if you want to retrieve a specific
> > sequence with
> > > a
> > > > particular ID...
> > > > What I want to do, is to submit a blast and then retrieve
> > the result and
> > > > then parse the result in oder to know what are the ID....
> > > > I already found in the NCBI site (
> > > > http://users.encs.concordia.ca/~f_kohant/ncbiblast/<http://users.encs.concordia.ca/%7Ef_kohant/ncbiblast/>)
> a
> > java interface
> > > but
> > > > the documentation is not so nice....and the link with
> > biojava is quit
> > > > obscure for me....
> > > >
> > > > could you help me please
> > > >
> > > > thanks for all
> > > >
> > > > Bertrand
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > 2007/9/4, Dickson Guedes < guedes at pmf.sc.gov.br>:
> > > > >
> > > > > Hi Bertrand,
> > > > >
> > > > >
> > > > > You may use a code like this:
> > > > >
> > > > >
> > > > > try {
> > > > > NCBISequenceDB impSequence = new NCBISequenceDB();
> > > > >
> > > > > Sequence mySequence =
> > impSequence.getSequence("156447465");
> > > > >
> > > > > System.out.print(
> > > > > mySequence.getAnnotation()
> > > > > .getProperty("description")
> > > > > .toString()
> > > > > );
> > > > > } catch (BioException e) {
> > > > > System.out.println(e.getMessage());
> > > > > }
> > > > >
> > > > >
> > > > > []s
> > > > > Guedes
> > > > >
> > > > > -----Mensagem original-----
> > > > > De: biojava-l-bounces at lists.open-bio.org
> > > > > [mailto:biojava-l-bounces at lists.open-bio.org] Em nome
> > de bertrand
> > > beckert
> > > > > Enviada em: terça-feira, 4 de setembro de 2007 06:10
> > > > > Para: biojava-l at lists.open-bio.org
> > > > > Assunto: [Biojava-l] How to launch a blast on ncbi
> > server via biojava?
> > > > >
> > > > > Hi,
> > > > >
> > > > > Sorry for this silly question, but I would like to know if it is
> > > possible
> > > > > to
> > > > > launch some blast via biojava on the ncbi server for an
> > example and
> > > also
> > > > > to
> > > > > retrieve the result as it is possible in in the bioperl project.
> > > > > I found some information in the biojava cookbook as
> > how to parse some
> > > > > blast
> > > > > file result but I didn't find any information/example
> > for launch blast
> > > on
> > > > > the ncbi server....
> > > > > Could you help me please
> > > > >
> > > > > Thanks
> > > > >
> > > > > Bertrand
> > > > > _______________________________________________
> > > > > Biojava-l mailing list - Biojava-l at lists.open-bio.org
> > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > > > >
> > > > >
> > > > > --
> > > > > Esta mensagem foi verificada pelo sistema de antivírus e
> > > > > acredita-se estar livre de perigo.
> > > > >
> > > > > Prefeitura Municipal de Florianopolis - PMF
> > > > > PMF.SC.GOV.BR
> > > > > --
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > Bertrand BECKERT
> > > > PhD student
> > > > IBMC - UPR 9002 du CNRS - ARN
> > > > 15, rue Rene Descartes
> > > > F-67084 STRASBOURG Cedex
> > > >
> > > > b.beckert at ibmc.u-strasbg.fr
> > > > bertrand.beckert at gmail.com
> > > >
> > > > _______________________________________________
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> > > >
> > >
> >
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