Bob Freeman | 5 Jun 19:06 2013

Re: Overlapping sets of coordinates?

No alignment -- I used PASA to generate (properly) align transcripts against a genome. Among the PASA
outputs is a tab-delimited file that lists the alignments of all my input transcripts in an almost GFF3
file like format. So I need to iterate through the alignments that are valid (one of the columns) and see if
any of these match (overlap, include, etc) the coordinates of certain gene models.

On Jun 5, 2013, at 12:03 PM, Brian Osborne <bosborne11 <at>> wrote:

> Bob,
> Flattery will get you everywhere.
> Are you saying that you have this mapping in the form of an alignment file of some kind?
> On Jun 5, 2013, at 10:53 AM, Bob Freeman <bobfreemanma <at>> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l <at>

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