[EMBOSS] backtranseq

[Nadeem Faruque]

Josh Cherry wrote:
> Nadeem Faruque wrote:
> 
> 
>>Returning a degenerate sequence would have the advantage (for some uses)
>>of being usable by normal DNA-savvy string-based search methods when
>>finding the peptide coding location in nucleic acid sequences rather
>>than having to use similarity searches.
> 
> 
> But this won't work the way some might hope due to the nature of the
> genetic code, specifically (in the standard code) the three amino acids
> that have six codons each (S, L, and R).  Consider serine, encoded by UCN
> and AGY.  Would you like this to be back-translated to WSN?  That matches
> all six serine codons but also ten non-serine codons.  Some people may
> still want to use it in a probe or primer though.

I was going to use Serine in my example but realised 'WSN' was a bit too degenerate to be a useful example.
I understand you could not roundtrip peptide->DNA->peptide with my suggested behaviour (as you can currently do with 
backtranseq), but you can do DNA->peptide->DNA in a usable form.
I'm sketchy about its potential use in oligo design, but given a degenerate backtranslation someone could possibly 
design oligos so as to avoid the more degenerate areas (esp for the 3' end of primers).  If they were to use backtranseq 
they would be ignorant of these regions.

Nadeem

-- 
S.M. Nadeem N. Faruque
EMBL Nucleotide Database Curation Team
EMBL Outstation
Tel: +44 1223 494611                     Fax: +44 1223 494472
The European Bioinformatics Institute    URL: http://www.ebi.ac.uk/
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Email for updates: update at ebi.ac.uk
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