[Biojava-l] question about BLAST output parsing

[Louise Ott]

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: 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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