[Biojava-l] question about BLAST output parsing

[Jiachen Xue]

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