[Bioperl-l] 3-frame and 6-frame translation

[Brian Osborne]

Barry,

Bio::SeqUtils.

# translate a sequence in all six frames
 @seqs = Bio::SeqUtils->translate_6frames($seq);


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 Barry Moore
Sent: Thursday, January 29, 2004 1:08 PM
To: bioperl
Subject: [Bioperl-l] 3-frame and 6-frame translation


Last night I was looking at methods in various bioperl modules trying to
come up to speed on the various ways to translate nt sequence in
bioperl.  I ran across two methods that, given a nt sequence (can't
remember if they took a string or an object), would return (as an array
or strings I think) either a 3-frame or 6-frame translation of the
sequence.  This morning I can't  find the module where those are located
again.  I think the module might have had "utilities" in the path, but
not sure.  I know about the translate method of a PrimarySeq object and
it's ability to specify frame, but still want to look more closely at
the other mystery module that I have now lost.  Does anyone know what
I'm talking about, and where it is?

This brings up a related question that had a similar post within the
last 24 hours.  My skill at searching the bioperl web site is terrible.
I just use the http://search.open-bio.org/ search site, but the search
results return almost (if not) exclusively postings to the bioperl list
that are usually 3+ years old.  I've tried just using Google limited to
the bioperl domain with only moderately better success.  The main thing
that keeps me frustrated is that my searches never seem to descend into
the module documentation where I might get a hit on a method
description.  Am I doing something wrong, or is this an intended
limitation of searching bioperl?

Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, Utah


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