Sorry i forgot : there is an example of using blast parser in here : http://biojava.org/wiki/BioJava:CookBook:Blast:Parser It should be enough for what you want to do.
> Date: Mon, 15 Mar 2010 19:09:50 -0400 > From: [email protected] > To: [email protected] > Subject: [Biojava-l] question about BLAST output parsing > > Hi, > > Thanks advance for help. > > For the following piece of text appearing in a blast output. How can I get > the fields of "Identities", "Positives", "Gaps" as well as the alignment > information, such as "DK V L+D + G +S + +++ +E GA+K+ L + AAPE" and > subject string? > > >sp|B9KAQ6.1|UPP_THENN RecName: Full=Uracil phosphoribosyltransferase; > AltName: Full=UMP > pyrophosphorylase; AltName: Full=UPRTase > Length = 209 > > Score = 32.0 bits (71), Expect = 9.7, Method: Compositional matrix > adjust. > Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 2/42 (4%) > > Query: 360 DKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLAS--AAPE 399 > DK V L+D + G +S + +++ +E GA+K+ L + AAPE > Sbjct: 124 DKEVFLLDPMLATGVSSVKALDILKENGARKITLVALIAAPE 165 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _________________________________________________________________ Consultez gratuitement vos emails Orange, Gmail, Free, ... directement dans HOTMAIL ! http://www.windowslive.fr/hotmail/agregation/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
