[EMBOSS] finding genes/features in flanks of region of interest

Jon Ison jison at ebi.ac.uk
Fri Feb 15 13:58:21 UTC 2008

Hi Shrish

As a starting point, you could have a look at getorf:

which will (optionally) return regions flanking START and / or STOP codons.

If you know an exact region of interest that can be specified
with -sbegin and -send for any input sequence.



> Hi!
> Does anyone know how to find genes in sequences flanking a region of interest? Most programs require the length of
> flanks to scan. We are interested in the nearest genes on either side, and maybe the distance of the gene to our
> region of interest.
> Shrish
> Dr. Shrish Tiwari
> E503, Centre for Cellular and Molecular Biology
> Uppal Road, Hyderabad - 500 007, INDIA
> Phone: 91-40-27192777
> Alternate email: shrish.geo at yahoo.com
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