Question: Stop Codons In Mega 5 Multiple Alignment With Muscle...
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gravatar for Winawer
6.3 years ago by
Winawer20
Australia
Winawer20 wrote:

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!

multiple • 5.1k views
ADD COMMENTlink written 6.3 years ago by Winawer20

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

ADD REPLYlink written 6.3 years ago by Neilfws48k

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?

ADD REPLYlink written 6.3 years ago by Winawer20
2
gravatar for Winawer
6.3 years ago by
Winawer20
Australia
Winawer20 wrote:

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.

ADD COMMENTlink written 6.3 years ago by Winawer20

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

ADD REPLYlink written 6.3 years ago by Giovanni M Dall'Olio26k
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