Question: Deleting Stop Codons
0
gravatar for Eric
6.7 years ago by
Eric90
Eric90 wrote:

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.

codon sequence conversion • 3.6k views
ADD COMMENTlink modified 2.6 years ago by wangqingqing0 • written 6.7 years ago by Eric90

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

ADD REPLYlink written 6.7 years ago by David W4.7k

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!

ADD REPLYlink written 2.6 years ago by wangqingqing0
0
gravatar for Pappu
6.7 years ago by
Pappu1.9k
Pappu1.9k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Pappu1.9k

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.

ADD REPLYlink written 2.6 years ago by st.ph.n2.4k
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