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

Barry Moore barry.moore at genetics.utah.edu
Thu Jan 29 13:08:02 EST 2004

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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