[EMBOSS] backtranseq

[Nadeem Faruque]

> See http://emboss.sourceforge.net/apps/ for application documentation.
> 
> transeq       Translates nucleic acid sequences.   (i.e. DNA -> protein)
> backtranseq   Back translate a protein sequence    (i.e. protein -> DNA)
...

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'

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.

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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