pssm.search from Bio.motifs not working with amino acid sequences
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5.7 years ago
stefano • 0

I am trying to find a motif out of a list of amino acid sequences.I am using the package Bio.motifs. I followed the documentation as in theBiopython Tutorial and Cookbook chapter 14.

Everything go smoothly and I generate the PWM and the PSSM out of my sequences. Then I wanted to use this PSSM to look for that motif in a new sequence. But when I try to use the method search (as in 14.6.2) with my PSSM I get this error:

ValueError: PSSM has wrong alphabet: IUPACProtein() - Use only with DNA motifs

So I have two question:

  • Is the package Bio.motifs suitable for proteins (from documentation is not clear anymore to me)? And can I trust the PSSM I generated?
  • How can I now use this PSSM to look for the motif? Is there another program or python package that allow me to do so? I searched online and I could not find anything so far.
motif pssm protein amino acid pwm • 1.9k views
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