[EMBOSS] backtranseq

[Gary Williams, Tel 01223 494522]

Peter Rice wrote:
> 
> Nadeem Faruque wrote:
> 
> > While backtranseq is very clever in predicting the cDNA sequence based on peptide sequence by choosing codons according
> > to useage, would it not be very useful to have the option for it to return an answer in degenerate bases?
> >
> > eg in human, the 'peptide' is simply 'M'
> > backtranseq returns the most likely codon used, ie 'ATG'
> > but since it could be TTG, CTG or ATG, it may be more useful for some people to return 'HTG'
> 
> Ummmm .... depends on the genetic code. In human I would expect ATG, in
> bacteria GCG is second schoice and NTG would be the possible result - but only
> for a start codon of course (just one of the complexities of backtranslating -
> I think we must avoid inventing a start codon if the protein doesn't start
> with 'M' because the numbering gets complicated).
> 
> As this would need a different input (a genetic code, rather than a codon
> usage file) I would make this a different program - not difficult to write,
> 
> Any good suggestions for a program name?

barebackseq

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522 
(UNTIL END OF JULY 2005)

E-mail: gareth.williams57 at ntlworld.com