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
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