[Bioperl-l] Blast Output Parsing

[Chris Fields]

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
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