Stop Codons In Mega 5 Multiple Alignment With Muscle...

Question

[Winawer]

Hello,

I'm pretty new to the bioinformatics space, so forgive the newbishness of the question. :-) I'm trying to do a multiple alignment of coding sequences for a protein I'm interested in, using Mega 5.05. Following the advice in Barry Hall's book, I'm trying to align the sequences using MUSCLE, aligning by codons. However, I keep getting an error during the alignment: "Stop codon(s) are found in the translated sequences. Please select a correct Genetic Code or coding frame." If I ignore the error and look at the translated protein sequences from the resulting alignment, I can't find any evidence of unidentified or termination codons within the sequences, just at the end (as I would expect). Am I misinterpreting the error, or if not, is there a way to figure out which sequence is causing the problem so I can decide what to do with it? (Or door number 3, in which the answer is about something I haven't anticipated?)

Thanks!

[Neilfws]

Perhaps the stop codons at the end are the problem? Can you get rid of them and try again?

[Winawer]

Well, I'll be damned. Of all the ... why would it view stop codons at the end of a coding sequence as being an error? Does that make sense somehow?

Answer 1

[Winawer]

Answering my own question: as pointed out by neilfws, the problem is that Mega notices the stop codons at the end and counts them as being an error. I don't know why that would be, but removing them does solve the problem.

[Giovanni M Dall'Olio]

thanks for sharing your answer with the rest of the community. Maybe other people will benefit from this discussion in the future.

[andorjkiss]

Do the stop codons have any influence on the alignment?