Conservation code
Conservation_code
http://compbio.cs.princeton.edu/conservation/
protein sequence conservation scoring tool
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.
Licensing
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Debian
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20 March 2013
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License: GPL-2.0+
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-
licenses/GPL-2".
Leaders and contributors
| Contact(s) | Role |
|---|---|
| John A. Capra | contact |
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Debian (Ref) (R) | https://tracker.debian.org/pkg/conservation-code | |
| Download | http://compbio.cs.princeton.edu/conservation/ |
Software prerequisites
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