[Bioperl-l] Alignment Blast parser

[Jason Stajich]

You want to retain it meaning what?
 Bio::SearchIO(-format => 'blast')
parses blast for you.

-jason
On Thu, 22 Jan 2004, Agrin, Nathan wrote:

> I need a way to retain the EXACT alignment found in a blast file.
> Ex-
>
>
> Query: 1   MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT
> 59
>            M+GRGK G  +  KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT
> Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
> 60
>
>
> Query: 60  AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP
> 117
>            AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP
> Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP
> 118
>
> I have tried everything to no avail.  AlignIO almost works out, but
> instead of doing a typical blast alignment, the best it can do is a
> clustalw like alignment.
>
> Any help is much appreciated.
>
> -Nate
>
> Nathan Agrin
> Research Associate
> UMass Medical Center
> 55 Lake Ave. N.
> Worcester MA, 01655
> (508)-856-6018
> nathan.agrin at umassmed.edu
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu