[BioPython] hydrofobic index

[Iddo]

(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
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