[Bioperl-l] Extract features from GFF

Hang hangsyin at gmail.com
Mon Oct 22 18:30:10 EDT 2007


I have a list of about 100,000 short genomic regions with paired start and end
coordinations on reference fly genome (R5.3). I also have GFF files from the
same genome release. I wonder how I can extract all overlapping features from
these regions.

For example:

region A is on chromosome 2L between 123,456 bp to 123,489 bp. What code should
I use to extract feature, like gene, CDS etc., that overlaps with this region?

Thank you in advance!

-- Hang

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