[BioPython] biophysical properties of proteins

[Andrew]

I've written a piece of code for parsing the AAindex database, which has 
tons of published amino acid indices and a cluster analysis of them.

The current version of my code is at:
http://members.optusnet.com.au/~a.j.perry/code/AAIndex.py

The aaindex file it reads is at:
ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1
(see http://www.genome.ad.jp/dbget/aaindex.html for details)

The code is a bit long to post here (and messy + embarrasing + 
unfinished etc), but if you are using amino acid indicies, I think its 
pretty useful. There is a usage example at the top which could be nicely 
integrated with Iddo's example.

It would be cool to be able to include this into biopython, but I think 
it would be simplest if the aaindex1 file could be distributed with 
biopython so it can work 'out-of-the-box' (it is 418 k) . . . whats the 
best way to go about this ??

Andrew Perry
Department of Biochemistry & Molecular Biology
University of Melbourne

Iddo Friedberg wrote:

>
> 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
> >
>
>