[Bioperl-l] Overlapping sets of coordinates?

[Bob Freeman]

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

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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





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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