[Bioperl-l] overlapping features

gabriele.bucci at unimi.it gabriele.bucci at unimi.it
Wed Mar 31 12:43:00 EST 2004

Hi all.
Need some help about the use of the method overlap (ensembl API). Say I would like to know if a slice in the genome overlaps a gene and where (exon, intron, UTRs), how could I achieve this? I was able to retrieve the gene,transcript and exon position relative to my slice, but I need something more direct like : "Yes your slice is located in the (Upstream,UTR,Exon,Intron,3'UTR,Downstream) this gene".

Can you tell me something useful?
Thanks a lot.


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