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How To Calculate Hydrophobicity Of Aminoacids With Biopython?

Hi,

How to calculate hydrophobicity (Kyte-Doolittle scale) of each amino acid sequence in my dataset by using a window size of 5 amino acids with biopython?

Your suggestions would be appreciated

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2 answers

Something like this?

from Bio.SeqUtils.ProtParamData import kd
from Bio.SeqUtils import ProtParam

my_seq="MAEGEITTFTALTEKFNLPPGNYKKPKLLY"
pa = ProtParam.ProteinAnalysis(my_seq)

print "K&D along the protein:"
for value in pa.protein_scale(kd, window=5):
    print "%.3f" % value

See also: http://lists.open-bio.org/pipermail/biopython/2004-July/002224.html

You can read this old post, describing how to apply the Kyte-Dolittle scale to a protein sequence: http://telliott99.blogspot.ch/2010/03/kyte-doolittle-hydrophobicity-plot-in.html

Unfortunately, the Kyte-Dollitle scale is something that comes from very old times in the history of science. It still used nowadays, but I don't know how much you can trust it.

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