[Biojava-l] question about BLAST output parsing

[Louise Ott]

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: xuejiachen at gmail.com
> To: biojava-l at lists.open-bio.org
> 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
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