[Bioperl-l] Overlapping sets of coordinates?

[Brian Osborne]

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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