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Gmane
From: Brian Osborne <bosborne11 <at> verizon.net>
Subject: Re: Overlapping sets of coordinates?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 5th June 2013 16:03:20 UTC (over 3 years ago)
Bob,

Flattery will get you everywhere.

Are you saying that you have this mapping in the form of an alignment file
of some kind?

BIO

On Jun 5, 2013, at 10:53 AM, Bob Freeman 
wrote:

> Dear knowledgeable & experienced community,
> 
> I've been racking my brains on this one and I'm sure it's been solved
before, but can't seem to find where/how to do this without major amounts
of custom coding: I have a set of transcripts mapped against a genome. I'd
like to know which transcripts overlap a given set of coordinates (e.g.
coordinates for a certain gene model). Is there an easy way to ascertain
overlap, non-overlap, partial overlap, etc. in BioPerl??
> 
> Thanks,
> Bob
> 
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Acorn Worm Informatics, Kirschner lab
> Dept of Systems Biology, Alpert 524
> Harvard Medical School
> 200 Longwood Avenue
> Boston, MA  02115
> 617/432.2294, vox
> 
> "Sorry I'm late. Oh, God, that sounded insincere. I'm late."
> 	-- Karen Walker, from Will and Grace
> 
> 
> 
> 
> 
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> 51 Downer Avenue, #2
> Dorchester, MA  02125
> 617/699.7057, vox
> 
> "Well, I'm thankful that I found a pharmacologist who is as dumb as a box
of hair."
> 	-- Karen Walker, from Will and Grace
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 
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