[Bioperl-l] Alignment Blast parser

[Agrin, Nathan]

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