[EMBOSS] backtranseq

[Josh Cherry]

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.

Josh

--
Joshua L. Cherry, Ph.D.
NCBI/NLM/NIH (Contractor)
jcherry at ncbi.nlm.nih.gov