Bug#690058: ITP: conservation-code -- tool to score protein sequence conservation
Package: wnpp
Severity: wishlist
Owner: Laszlo Kajan <lkajan@rostlab.org>
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
* Package name : conservation-code
Version : 20110309.0
Upstream Author : John A. Capra <tonyc@cs.princeton.edu>, Mona Singh <mona@cs.princeton.edu>
* URL : http://compbio.cs.princeton.edu/conservation/
* License : GPL-2.0+
Programming Lang: Python
Description : protein sequence conservation scoring tool
Enhances : concavity
This package provides score_conservation(1), a tool to score protein sequence
conservation.
.
The following conservation scoring methods are implemented:
* sum of pairs
* weighted sum of pairs
* Shannon entropy
* Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
Valdar and Thornton 2001)
* relative entropy with property groupings (Williamson 1995)
* von Neumann entropy (Caffrey et al 2004)
* relative entropy (Samudrala and Wang 2006)
* Jensen-Shannon divergence (Capra and Singh 2007)
.
A window-based extension that incorporates the estimated conservation of
sequentially adjacent residues into the score for each column is also given.
This window approach can be applied to any of the conservation scoring
methods.
.
The program accepts alignments in the CLUSTAL and FASTA formats.
.
The sequence-specific output can be used as the conservation input for
concavity.
.
Conservation is highly predictive in identifying catalytic sites and
residues near bound ligands.
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)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=6Kbc
-----END PGP SIGNATURE-----
Reply to: