[Bioperl-l] six frame translation to gff?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Oct 24 15:18:46 EDT 2012


Not a Bioperl solution, but sixpack from Emboss will output gff
http://emboss.sourceforge.net/apps/cvs/emboss/apps/sixpack.html

You could probably do something tricky with a regex to chunk the sequence into frames and $my_seq_object->translate
http://www.bioperl.org/wiki/HOWTO:Beginners#Translating

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
Sent: Thursday, 25 October 2012 6:06 a.m.
To: bioperl-l at bioperl.org; GMOD GBrowse List
Subject: [Bioperl-l] six frame translation to gff?

Is there a simple way to do this?  For teaching we want to illustrate how all possible reading frames are NOT real CDS features. Most browsers display the 6 frame translation, but I would like to convert this information to GFF so they can be viewed, filtered etc.

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



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