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 [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
