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// A PWM with gapped alignments in Biopython
// August 9, 2011 at 11:28 AM

http://stackoverflow.com/questions/6998727/a-pwm-with-gapped-alignments-in-biopython
I'm trying to generate a Position-Weighted Matrix (PWM) in Biopython from Clustalw multiple sequence alignments.  I get a "Wrong Alphabet" error every time I do it with gapped alignments.  From reading the documentation, I think I need to utilize the Gapped Alphabet to deal with the '-' character in gapped alignments.  But when I do this, it still doesn't resolve the error.  Does anyone see the problem with this code, or have a better way to generate a PWM from gapped Clustal alignments?

from Bio.Alphabet import Gapped
alignment = AlignIO.read("filename.clustalw", "clustal", alphabet=Gapped)
m = Motif.Motif()
for a in alignment:
    m.add_instance(a.seq)
m.pwm()


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