Create protein translation from alignment?

[k-gun12]

I have a multiple alignment of a rather large protein. I also have a contig in my assembly that contains that protein, but there are many introns/frameshifts that make translating it difficult. Is there a tool around that will generate a "consensus" translation from the already-existing protein alignment? i.e take my contig, translated in 6-frames, and line up whatever hits across the MSA? (That's what I'm doing by hand right now...)

Thanks!!

[MG1655]

I have a multiple alignment of a rather large protein. I also have a contig in my assembly that contains that protein, but there are many introns/frameshifts that make translating it difficult. Is there a tool around that will generate a "consensus" translation from the already-existing protein alignment? i.e take my contig, translated in 6-frames, and line up whatever hits across the MSA? (That's what I'm doing by hand right now...)

Thanks!!

While not exactly what you want, exonerate with the protein2genome model option might get you close.

It will take in one protein sequence and then align it to your DNA, while modeling the introns. The website details the many other options available

http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html

Best of luck

[k-gun12]

Thanks- I'll take a look. Basically I'm annotating a horizontal gene transfer into a eukaryote genome of a bacterial gene. It's now full of introns where it used to be in a single frame