[EMBOSS] backtranseq

[Nadeem Faruque]

> As for the problem cases like Serine, maybe an option to make instead of a 
> sequence with ambiguity symbols a regular expression that exactly matches 
> the allowed codons ? The utility of this may be limited, but you could 
> e.g. if you have a peptide use the backtranslation with the program dreg to
> search the corresponding CDS in a piece of DNA.

I think we'd be better off with plain old IUPAC rather than venturing into more comples systems or we'll end up with 
weighted matrices or even HMM's.
The advantage of IUPAC is of course that you can plug it into most other programs.

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/
Email for data submissions: datasubs at ebi.ac.uk
Email for updates: update at ebi.ac.uk
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