#49 Sixpack question
Subject: [emboss-bug] Sixpack question
From: mark.rose@syngenta.com
Date: Tue, January 8, 2008 9:05 pm
To: emboss-bug@emboss.open-bio.org
Priority: Normal
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Hello
I've been trying to use the EMBOSS sixpack program to identify (and
display them exclusively in the outfile) ORFs with a minimum size of 150
bases that begin with a ATG codon and, in addition to the standard
output in html format, also output in a file all ORFs meeting these
criteria.
I use the following command line (for example):
sixpack -sequence my_sequence_file -outfile testoutfile -mstart
-orfminsize 50 -auto -html -outseq testoutseq -highlight 1-10
What I get back in the outfile however shows all ORFs exceeding 50
encoded amino acids regardless of whether they begin with ATG (ORFs
starting with ATG only appear to be listed in the outseq file).
This is not the behavior I expected using the mstart flag. Am I doing
something wrong? Is there a way to achieve what I seek with this tool.
Thanks for your help
Mark
Dr. Mark Rose
Scientist III
Bioinformatics
Syngenta Biotechnology, Inc.
3054 Cornwallis Rd.
RTP, NC 27709
919-541-8579
