[BioPython] hydrofobic index

[Iddo]

Iddo wrote:

If I didn't make it clear, I fixed the bug, so the new ProtParam should 
be checked out of CVS.

Also, please correct line 4 in the code I gave to:

print "GRAVY", pa.gravy()

>
> (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
>>  
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> BioPython mailing list  -  BioPython at biopython.org
>> http://biopython.org/mailman/listinfo/biopython
>>  
>>
>
>


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo