Deleting Stop Codons

Question

[Eric]

Hello,

I collect sequences for multiple species from UCSC Genome Browser. In order to enter my sequences into HyPhy, I need to remove all stop codons (or at least those that HyPhy recognizes as stop codons). Is there a way to remove the stop codons from the sequences to prepare them for HyPhy?

Thanks.

[David W]

codon models only make sense for protein coding sequences. If you have in-frame stops you should make sure you have only exonic sequence, check your alignment and check that you're setting the appropriate genetic code in HyPhy

[wangqingqing]

Hello， I have a similar problem。In big data,I must delete the stop codons in the sequence.So,can you give me some suggestions?

Thanks!

Answer 1

[Pappu]

try in shell: sed 's/TAA//g' < inputfilename > outputfilename or similar e.g. echo ATGCTAAAGC | sed 's/TAA//g' I am not sure if it answers your question.

[st.ph.n]

This would be dangerous because the sed command would remove ALL 'TAA' globally. The best approach is the search each sequence in a sliding window of 3bp, and search for a string match for 'TAA', 'TGA', 'TAG'. Unless you already have trimmed ORFs, you can simply trim off the last 3bp of each sequence.