[EMBOSS] transeq and ambiguous codons

[Scott Markel]

Peter,

Answer to question #2: run the program embossversion.

> embossversion
Writes the current EMBOSS version number to a file
6.0.1

Scott

Scott Markel, Ph.D.
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> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-
> bio.org] On Behalf Of Peter
> Sent: Wednesday, 08 July 2009 2:50 PM
> To: emboss at lists.open-bio.org
> Subject: [EMBOSS] transeq and ambiguous codons
> 
> 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
> 
> First consider the following example, the codon TAN, which can be TAA,
> TAC, TAG or TAT which translate to stop or Y. Therefore the
> translation of TAN should be "* or Y", and EMBOSS transeq opts for
> "X". Which is fine:
> 
> $ transeq asis:TAATACTAGTATTAN -stdout -auto
> >asis_1
> *Y*YX
> 
> Similarly for the codon TNN, again EMBOSS transeq opts for "X" because
> this could be a stop codon, or W, or F, or L, or S, or Y or C! Again,
> this is fine:
> 
> $ transeq asis:TNN -stdout -auto >asis_1
> X
> 
> 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
> 
> I think this is a bug.
> 
> However, I am aware that the machine I tried this on is rather old,
> and I don't actually know which version of EMBOSS it is. How can I
> find out? As far as I know, there is no "-version" or "-v" or
> "--version" switch, and the "-help" information doesn't include this
> important piece of information. Nor is this in the FAQ:
> http://emboss.sourceforge.net/docs/faq.html
> 
> So that makes two questions - how should transeq translate "TRR", and
> how do I check the version of EMBOSS?
> 
> Thanks,
> 
> Peter C.
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