Hi!
I had sent the message attached earlier and received no reply. Is there no interest in the modifications suggested for backtranseq or did the message not reach anyone, which is possible due to the unreliability of our mail system.
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@yahoo.com


    
        
            
-- Original Message --
From: shrish@ccmb.res.in
To: emboss@emboss.open-bio.org
Date: Wed, 23 Jul 2008 12:20:05 +0530 (IST)
Subject: requests for backtranseq

            Hi!
I would like to make some suggestions to enhance the utility of backtranseq:
- At present backtranseq uses the most preferred codon exclusively for a given amino acid. It would be nice if it could use all synonymous codons with probabilities defined by their usage. For example, codon usage for Ala in humans is 0.10, 0.22, 0.28 and 0.40 for GCG, GCA, GCT and GCC respectively. So, all 4 codons could be used for Ala, with GCC being used most often and GCG the least number of times.
- Allow for uniform usage of all synonymous codons, for example to carry out an in-silico experiment by eliminating codon preference.
- Also, I find if I give backtranseq a file in multi-fasta format, it translates only the first sequence.
Thanks.
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@yahoo.com