On Wed, May 26, 2010 at 7:50 PM, Justin Havird <jchav...@gmail.com> wrote: > > Hi, > > I am trying to align nucleic acid sequences based on amino acid alignments > using the program tranalign. The program normally works fine for me, but > lately I have been using mitochondrial genes and am beginning to run into > problems. > > These occur when the nucleotide sequence does not match the amino acid > translation exactly. For example, in the prawn M. japonicus, the first amino > acid (MET) in the COX1 gene is encoded by the codon "ACG" rather than the > typical "ATG". Tranalign doesn't recognize ACG as encoding MET, so it throws > up this message: > > Error: Guide protein sequence M. japonicus not found in nucleic sequence M. > japonicus > > These errors occur on a taxa by taxa basis and are usually because of the > first codon. However, the error also occurs when the nucleotide sequence has > an ambiguous nucleotide (e.g., Y), even if the ambiguous nucleotide position > doesn't affect the translation (e.g., both GTC and GTT = VAL). I can usually > pinpoint the error to a specific nucleotide/codon like in these examples. > > These errors are relatively rare, but happen more frequently in some groups > (inverts and fishes mostly). > > So, does anyone know a way to "relax" the tranalign translation rules to > circumvent this problem? Or have another program/solution?
Hi Justin, This might be a silly question, but have you used the tranalign argument -table to specify which genetic code table to use? I'd guess you probably want the Vertebrate Mitochondrial Code instead of the Standard Code. Peter C. _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
