[Bioperl-l] six frame translation to gff?

[Smithies, Russell]

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



_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================