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

enter image description here

Extra info

  • I am using Python2.7 and often use Biopython
  • My users are likely to run the programs from Windows machines
evolution protein • 4.3k views
ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by a1ultima710
1

Doing sliding window dn/ds analyses is not a good idea: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003746

ADD REPLYlink written 5.3 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 5.3 years ago • written 5.3 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 27 days ago by mariamcurbelo20610
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