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? I think the user from the message below had a similar problem, but I see no answer. :( Thanks! Justin >From Nov 12, 2006: > Hello - I'm trying to use tranalign to align DNA sequences but it > keeps throwing errors. I tested it on the example input files from > the documentation web pages and those work fine. > > Error: Guide protein sequence SS1G01814 not found in nucleic sequence > SS1G01814 > <snip> > it throws the same error for every pair of proteins in the file > > here are the sequence names in the files. I can supply the full > files if anyone thinks they can help. Yes, please send the full files to emboss-bug at emboss.open-bio.org The message is not an ID mismatch - it says the protein sequence did not match the DNA sequence. regards, Peter Rice ********************************************************************** Justin C. Havird Department of Biological Sciences & Cellular and Molecular Biosciences Program Auburn University 101 Life Science Building Auburn, AL 36849 Tele # (334) 844-3223 Fax # (334) 844-1645 Email: jhav...@auburn.edu Lab Website: http://www.auburn.edu/~santosr/<http://www.auburn.edu/%7Esantosr/> ********************************************************************** _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss