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

[Mark Schreiber]

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
>
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