[Biojava-l] How to launch a blast on ncbi server via biojava?

[bertrand beckert]

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/
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/) 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
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>