[EMBOSS] transeq and ambiguous codons

[Peter Rice]

Peter C. wrote:
> Hi all,
> 
> Something I mentioned to Peter Rice in passing at BOSC/ISMB 2009 was
> I'd found an oddity in transeq with certain ambiguous codons which
> testing Biopython's translations. Here is a specific example (but I
> suspect there are more). For reference, I am expecting EMBOSS transeq
> to be using the NCBI tables:
> http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Yes, those are our source.

> However, consider the codon TRR. R means A or G, so this can mean TAA,
> TGA, TAG or TGG which translate to stop or W (both EMBOSS and the NCBI
> standard table agree here). Therefore the translation of TRR should be
> "* or W", which I would expect based on the above examples to result
> in "X". But instead EMBOSS transeq gives "*":
> 
> $ transeq asis:TAATGATAGTGGTRRTNN -stdout -auto
>> asis_1
> ***W*X

Hmmm... something odd there. TRA translates as 'X'.

I will take a look, but we are bundling the 6.1.0 release so (unless I am 
very quick) any resolution will be a patch after the release.

> So that makes two questions - how should transeq translate "TRR", and
> how do I check the version of EMBOSS?

Scott got there first (different time zone I assume :-) with the suggestion 
of embossversion.

Meanwhile .... are there any translation utilities we could usefully 
include in a future version?

I am already contemplating one to report the translations of ambiguous 
codons, just for information in tracking and debugging translation tables - 
and explaining transeq and other applications to new users.

regards,

Peter Rice