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.motifssuitable 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.