Brian Osborne | 5 Jun 18:03 2013
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Re: Overlapping sets of coordinates?

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 <bobfreemanma <at> speakeasy.net> 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
> 
> 
> 
> 
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Gmane