Question: Determining the correct reading frames for transcripts for dn/ds calculation
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gravatar for shreyasibiswas88
2.0 years ago by
United States
shreyasibiswas8830 wrote:

Hi everyone,

I am trying to calculate genome-wide dn/ds ratio between two closely related rat species using PAML. I have genome co-ordinates for transcript orthologs for the two species. However, I am not able to figure out how to decide the reading frame for translating the sequences in to amino acid sequences. Currently, I am translating into reading frame 1 for all genes on forward strand and into reading frame 6 for all on reverse strand. I know this is gross approximation. Can anyone give me any ideas on how I could tackle this issue? Where can I find information on transcript specific reading frame? I am ignoring the problem of alternate splicing for now.

Without the information on reading frames, I am ending up with biased dn/ds ration. Please help me. Thank you.

ADD COMMENTlink written 2.0 years ago by shreyasibiswas8830

You just want the sequences of all the transcripts first?

ADD REPLYlink written 2.0 years ago by jrj.healey13k

I have the nucleotide sequences of all transcripts. I can't decide which reading frame to translate each one into. Should I select the longest ORF for each transcript?

ADD REPLYlink written 2.0 years ago by shreyasibiswas8830

It is typical to take the longest ORF. But here is a relevant study.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by microfuge1.1k
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