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 <[EMAIL PROTECTED]>: > > 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: > > > > > > 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: [EMAIL PROTECTED] > > > [mailto:[EMAIL PROTECTED] Em nome de bertrand > beckert > > > Enviada em: terça-feira, 4 de setembro de 2007 06:10 > > > Para: [email protected] > > > 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 - [email protected] > > > 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 > > > > [EMAIL PROTECTED] > > [EMAIL PROTECTED] > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
