[EMBOSS] backtranseq
Peter Rice
pmr at ebi.ac.uk
Thu Jul 21 14:00:30 UTC 2005
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?
> 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. I could also see it being useful for designing PCR primers within coding regions.
... which leads on to whether EMBOSS should include such programs :-)
regards,
Peter Rice
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