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. Principal Bioinformatics Architect email: smar...@accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Vice President, Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics > -----Original Message----- > From: emboss-boun...@lists.open-bio.org [mailto:emboss-boun...@lists.open- > bio.org] On Behalf Of Peter > Sent: Wednesday, 08 July 2009 2:50 PM > To: emboss@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. > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss