Package: wnpp Severity: wishlist Owner: Laszlo Kajan <lka...@rostlab.org>
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 * Package name : conservation-code Version : 20110309.0 Upstream Author : John A. Capra <to...@cs.princeton.edu>, Mona Singh <m...@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) iQIcBAEBAgAGBQJQdEEGAAoJEJvS1kCaDFL6ABkP+gJtgskydA+sOOf5Hi9/AYvQ i30VuQUVpY5uDIrxJ+o1c66wGHIzNzvLP+IVnCSDdK0BX1tLb2QqGMGRo32jG/yE K6jpfRyRwKMiZ8hZ9tM5w78NiJt5vSWyc6unGZdIRcpEIZVBU9T2joxmxNluu4z5 PI/jXxwMSqXQNY1NuhjosRpY0F5nltFSrjQAF3SFT1QUCpEGfmZKMaxvniP3ubeg dbPqPcDE8VgZFxMIKBB+FnGGb+QIoKYrP621Vx+FRrnv23Gd8vhidYEbAsXRXU7U gVP0k+RayjuikNGeZ+Bwm00oyy8/ehXKjsufG2e/FCo/G1dW3LmA+gUw0yZQbeXK 5WDdoiVDsgzlyAqnbVljiGIHoA8a9azu5Ta2/pyyPj0a2YB16o8V4XnWDC/N6WIQ 5C4gbpc4M0tA4yP/eCFkAwVKGr8BH4REApkDR7XqzcmVXVz2xQIqnea7SSea2dTc D2bednPxJh3C4eOOvhmDT5meg82/xfCJxIRyEcLon7g7bGBveGRhVA49W/Wxitph app1tsOp4NE9m5z5yIE83ZtdLrvAhaWib63JGf+9tsDkdWzVVnHORGiCUC6TRy7t YGz3D5+fi0GHEnJF0wpu/Yk2G2TWxnZ/3sQ2IrE9/IMorYLLM+szKns5rqdff9XY 7Fdtl/aJ3vKorM1wJSqx =6Kbc -----END PGP SIGNATURE----- -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121009152149.2728.83411.reportbug@debian-unstable.rostclust
