[BioPython] biophysical properties of proteins

[Iddo Friedberg]

Hi Fabien,

Do you mean an application which indexes hydrophobicity along a protein
sequence? Or something else?

If the former, then you will need to set your own indexes, according to
your preferences. then it's just a matter of doing:

-------------------- CUT HERE -------------
from Bio import FASTA

hp_index = {'A': -0.3, 'C': -0.1,...,'Y':0.4} # hydrophobic aa's are
                                               # negative here use your
                                               # own scale
def my_hp_search(fasta_file_path):
     my_seq = FASTA.FastaReader(open(fasta_file_path)).next()
     hp_seq = [(aa,hp_index[aa]) for aa in my_seq]
     return hp_seq
---------------- END CODE --------------------

hp_seq contains a list of tuples: (aa, hydrophobicity-index of that aa)

If that is _not_ what you meant, give a holler.

Iddo


Fabien Crozet wrote:
 > Hi all,
 > are there anything in biopython to do protein hydrophilicity / 
hydrophobicity search?
 > I can't find any informations about that...
 > Thanks in advance,
 > Fabien
 >


-- 
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) 646 3171
http://bioinformatics.ljcrf.edu/~iddo