[Bioperl-l] search for only C-terminal degenerate motifs

[Brian Osborne]

Lucas,

I don't think a script exactly like this exists in Bioperl but certainly the
means to write this script does. A good start might be the SearchIO HOWTO
(bioperl.org/HOWTOs). The combination of SearchIO and StandAloneBlast
(section III.4.5 of the bptutorial) enables you to run BLAST and parse the
results. The details of the C-terminal match should be straightforward, I
think, but it depends on your familiarity with Perl.

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 Lucas Carey
Sent: Thursday, October 09, 2003 6:48 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] search for only C-terminal degenerate motifs

Hi,
I'm not sure if this is the correct list, but I figured someone here would
be able to help me.
I'd like to use blast to search for a protein motif within a certain number
of residues of the C-terminus. What is the best way to go about doing this?
It seems like someone would have already had to do this, and written
software to do it. That's what made me think of bioperl.
-Lucas
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