[Bioperl-l] Blast Output Parsing

[Prabu R]

It works great

Thanks a lot Mr.Chris.

R. Prabu

On 7/20/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> Grab the HSPs, then use get_aln() to generate a Bio::SimpleAlign object.
> You can then use Bio::AlignIO to generate the alignment output if needed,
> or
> use the Bio::SimpleAlign methods to get what you want.
>
> http://www.bioperl.org/wiki/HOWTO:Beginners
>
> http://www.bioperl.org/wiki/HOWTO:SearchIO
>
>
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SimpleAlign
> .html
>
> Chris
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Prabu R
> > Sent: Thursday, July 20, 2006 11:02 AM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Blast Output Parsing
> >
> > Dear All!
> >
> > I am now trying to parse a Blast output using PERL.
> >
> > I have to extract each alignment and have to parse the alignment. I
> mean,
> > I
> > have to check whether a particular part of the given sequence got
> aligned
> > 100%.
> >
> > Anybody please tell me what module in PERL I have to use for getting
> this.
> >
> > I've tried Bio::SearchIO.  But I didnt get any method to get the
> > alignment.
> >
> > Kindly help.
> >
> > Thanks,
> > R. Prabu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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