[EMBOSS] Tranalign relaxation?

[Peter]

On Wed, May 26, 2010 at 7:50 PM, Justin Havird <jchavird at 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.