[Biojava-l] question about BLAST output parsing

[Andreas Prlic]

Yea, the BioJava Blast parser has not been maintained in quite a while.
Probably parsing the XML output of Blast is the thing to do nowadays. About
Biojava3: the wiki documentation is a bit behind, the code is now in the
main biojava-trunk and development has been quite active over the last
months.

Andreas

On Tue, Mar 16, 2010 at 2:20 AM, Louise Ott <anjolou at hotmail.com> wrote:

>
>
> 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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