Hello, I tried to use the biojava blast parser myself but i didn't find a way to get back these informations.If your blast result can be in xml, you should try to use jaxb to parse it (this is what i used).There are already some code for marshall/unmarshall in the biojava3 project.I give you the link, but it seems to be dead right now : http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/branches/biojava3 http://www.biojava.org/wiki/BioJava3_project Have a nice day, Louise
> 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 _________________________________________________________________ Hotmail arrive sur votre téléphone ! Compatible Iphone, Windows Phone, Blackberry, … http://www.messengersurvotremobile.com/?d=Hotmail _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
