sm_pam250.c
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- /*
- * ===========================================================================
- * PRODUCTION $Log: sm_pam250.c,v $
- * PRODUCTION Revision 1000.0 2004/02/12 22:05:44 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [CORE_001] Dev-tree R1.1
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: sm_pam250.c,v 1000.0 2004/02/12 22:05:44 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Author: Aaron Ucko (via ./convert_scoremat.pl)
- *
- * File Description:
- * Protein alignment score matrices; shared between the two toolkits.
- *
- * ===========================================================================
- */
- #include <util/tables/raw_scoremat.h>
- /* This matrix was produced by "pam" Version 1.0.7 [01-Feb-98] */
- /* using Dayhoff et al. (1978) mutability data. */
- /* PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 */
- /* Expected score = -0.844, Entropy = 0.354 bits */
- /* Lowest score = -8, Highest score = 17 */
- static const TNCBIScore s_Pam250PSM[24][24] = {
- /* A, R, N, D, C, Q, E, G, H, I, L, K,
- M, F, P, S, T, W, Y, V, B, Z, X, * */
- /*A*/ { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1,
- -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8 },
- /*R*/ { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3,
- 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8 },
- /*N*/ { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1,
- -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8 },
- /*D*/ { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0,
- -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8 },
- /*C*/ { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5,
- -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8 },
- /*Q*/ { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1,
- -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8 },
- /*E*/ { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0,
- -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8 },
- /*G*/ { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2,
- -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8 },
- /*H*/ { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0,
- -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8 },
- /*I*/ { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2,
- 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8 },
- /*L*/ { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3,
- 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8 },
- /*K*/ { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5,
- 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8 },
- /*M*/ { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0,
- 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8 },
- /*F*/ { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5,
- 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8 },
- /*P*/ { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1,
- -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8 },
- /*S*/ { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0,
- -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8 },
- /*T*/ { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0,
- -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8 },
- /*W*/ { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3,
- -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8 },
- /*Y*/ { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4,
- -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8 },
- /*V*/ { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2,
- 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8 },
- /*B*/ { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1,
- -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8 },
- /*Z*/ { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0,
- -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8 },
- /*X*/ { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1,
- -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8 },
- /***/ { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
- -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1 }
- };
- const SNCBIPackedScoreMatrix NCBISM_Pam250 = {
- "ARNDCQEGHILKMFPSTWYVBZX*",
- s_Pam250PSM[0],
- -8
- };