Question: Sliding Window Ka/Ks (Dn/Ds) Analysis Via Python?
gravatar for a1ultima
5.7 years ago by
a1ultima710 wrote:

I am working in Python and performing Ka/Ks (dN/dS) ratio analysis.

I would like to ask for any suggestions for how to go about performing "within gene" or "sliding window" Ka/Ks analysis, such that a Ka/Ks ratio can be given for positions along the gene sequence.

This MATLAB tutorial really sums up exactly what I need, but I am obliged by my boss to use Python.

Anticipated output example

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Extra info

  • I am using Python2.7 and often use Biopython
  • My users are likely to run the programs from Windows machines
evolution protein • 4.6k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by a1ultima710

Doing sliding window dn/ds analyses is not a good idea:

ADD REPLYlink written 5.7 years ago by karl.schmid20

thank you very much for this gem @karl.schmid, but indeed we plan to use sliding windows more for visual understanding as the paper suggests

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by a1ultima710

Hi, 5 years later I have the exact same problem...did you figure it out? Thanks in advance

ADD REPLYlink written 5 months ago by mariamcurbelo20610
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