[Bioperl-l] getting alignments out of blast reports

Brian Osborne brian_osborne at cognia.com
Mon Jan 27 08:54:20 EST 2003


The SearchIO HOWTO doesn't give all the details, we'll change that. Please
look at the attached script, it shows all the values returned by the Result,
Hit, and HSP objects. You'll see that HSP's query_string and hit_string
methods get you the sequences you want. Or did you want an actual alignment?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Nandita Mullapudi
Sent: Friday, January 24, 2003 5:05 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] getting alignments out of blast reports

can i use Search::IO to get alignments (i.e amino acid seqs of
query and hit)  out of blast reports for those that fulfill given criteria
(given e- value..etc.)? i dont see a parameter name for it in the
or, i'm missing it- on a cold friday evening in georgia!

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