[BioPython] hydrofobic index
Iddo
idoerg at burnham.org
Tue Jul 20 12:39:19 EDT 2004
(When going after your question, I actually found a bug in ProtParam. So
please check it out of the CVS).
The module you should use is: Bio.SeqUtils.ProtParam.py
Try this:
from Bio.SeqUtils import ProtParam
my_seq="MAEGEITTFTALTEKFNLPPGNYKKPKLLY"
pa = ProtParam.ProteinAnalysis(my_seq)
print "GRAVY", pa.gravy
print "K&D along the protein":
for i in pa.protein_scale(ProtParamData.kd, 9, 0.4):
print "%.3f" % i
HTH,
Iddo
Ernesto wrote
>Hi all,
>do you know if there is a biopython function to calculate the Kyte-Doolittle hydrofobic index? (Just the score for each site, not the plot)
>
>Many thanks
>
>Ernesto
>
>
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--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
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http://ffas.ljcrf.edu/~iddo
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