Solving Stop Codons

Question

[lmumladze]

Hi I have D-loop CO1 sequences gained from automated sequencer. I export abi fails to fasta format and then import in MEGA to align and analyze. However, after alignment, sequences are includes stop codons. what can I do to correct my data? I tried to shift frame but there are lots of gaps within the sequences after alignment. I am fully confused. can anyone suggest what can I do or indicate proper literature? I could not find solutions in various introductory books in phylogenetics and bioinformatics

[David W]

If you really had stop codons you would need to think about whether you'd amplified the gene your were aiming for. Since the d-loop isn't protein-coding you can't have stop (or any other) codons.

[Neilfws]

"abi fails"? Do you mean "abi files"? Sounds like the simplest solution would be to remove stop codons from the sequences before alignment.

Answer 1

[lmumladze]

Thank you very much. I am new for this kind of work. As I understood if I have sequenced d-loop, it may show some stop codons after translation. However this is not a problem as it is not a protein coding. This further means that I can continue work on this sequences and upload in gen-bank.