[Bioperl-l] Alignment Blast parser

[Agrin, Nathan]

Yes exactly

-Nate

-----Original Message-----
From: Brian Osborne [mailto:brian_osborne at cognia.com] 
Sent: Thursday, January 22, 2004 2:24 PM
To: Jason Stajich; Agrin, Nathan
Cc: bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] Alignment Blast parser

Jason,

I think he wants to print out the exact same alignment as you see in the
BLAST report, which you can't do using AlignIO.

Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2"
business as well?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
Sent: Thursday, January 22, 2004 2:14 PM
To: Agrin, Nathan
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] Alignment Blast parser

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
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