[Biojava-l] question about BLAST output parsing

[Mark Schreiber]

I generally don't recommend parsing the standard BLAST output as it keeps
changing subtly . Best to parse one of the tabular formats or the XML
output.

- Mark

On Tue, Mar 16, 2010 at 11:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> 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
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > 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  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>