Hi Bernd, not sure if you got a reply to your mail off-list. Did you manage to solve your problem in the meanwhile?
Andreas On Wed, Jul 29, 2009 at 6:16 AM, Bernd Jagla <[email protected]> wrote: > Hi, > > > > I am new to BioJava. I want to test what is going on here in order to > potentially integrate it with KNIME. > > My first project is parsing BLAST output for large files. The example in > the > codebook is very good and I had no problems integrating everything in > Eclipse and geting it to work. > > > > Now here is my problem: > > I am interested in parsing the summary table in the beginning of the > blast-output, and I haven't found a way to get at this information. > > > > I am blasting short sequences (20nt - 300nt) against genomic databases > (mouse/human/refseq/miRBase). I want to know if a given sequence (out of a > set of sequences) aligns to a specific genome with high identity. I want to > then separate the input source fasta file into a set that aligns to the > genome and one that doesn't (potentially another list of dubious sequences > where there is no clear answer). For this I only need the length of the > query sequence and score and the first few characters of the header line. > > At least that's the way I am currently doing it. I have set the blast > parameters to only give me the first alignment, but the first 50 or so in > the summary. > > > > Any help, comments are appreciated. > > > > Thanks, > > > > Bernd > > > > > > > > > > > > Bernd Jagla > Bioinformatician > > Institut Pasteur > Plate-forme puces a ADN > Genopole / Institut Pasteur > 28 rue du Docteur Roux > 75724 Paris Cedex 15 > France > > > <mailto:[email protected]> [email protected] > > > tel: > > > < > http://www.plaxo.com/click_to_call?lang=en&src=jj_signature&To=%2B33+%280%2 > 9+140+61+35+13&[email protected]<http://www.plaxo.com/click_to_call?lang=en&src=jj_signature&To=%2B33+%280%2%0A9+140+61+35+13&[email protected]>> > +33 (0) 140 61 35 13 > > > > > > _______________________________________________ > 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
