[Bioperl-l] Protein Sequence QSARs

[Mark A. Jensen]

Hi Brett--
I doubt if anything this specialized exists in BioPerl.
I'd say go for it, but R may be better suited for the calculations you
want to do. For dealing with matrices, you may want to check out
the Bio::Matrix namespace.
cheers Mark
----- Original Message ----- 
From: "Brett Bowman" <bnbowman at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, September 07, 2009 4:17 AM
Subject: [Bioperl-l] Protein Sequence QSARs


I've been working on a script for my personal edification for annotating
protein sequence for QSARs, as described in the paper below, because I
didn't see anything in Bioperl to do it for me.  Essentially converting a
protein sequence of length N into a numerical matrix of size 3-by-N by
substitution, and then calculating the auto- and cross- correlation values
for various for a lag of L amino acids.  I was considering turning it into a
full blown module, but I wanted to ask if A) it had been done before and I
had just missed it, and B) whether anyone other than me would find such a
module useful.

Wold S, Jonsson J, Sjöström M, Sandberg M, Rännar S: * DNA and peptide
sequences and chemical processes multivariately modeled by principal
component analysis and partial least-squares projections to latent
structures. **Anal Chim Acta* 1993, *277**:*239-253.

Brett Bowman
bnbowman at gmail.com
Woelk Lab, Stein Cancer Research Center
UCSD/SDSU Joint Program in Bioinformatics

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