sm_pam30.c

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: sm_pam30.c,v $
 * PRODUCTION Revision 1000.0  2003/10/29 16:04:25  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.1
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: sm_pam30.c,v 1000.0 2003/10/29 16:04:25 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 1.0.6 [28-Jul-93] */
/* PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574 */
/* Expected score = -5.06, Entropy = 2.57 bits */
/* Lowest score = -17, Highest score = 13 */

static const TNCBIScore s_Pam30PSM[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*/ {  6, -7, -4, -3, -6, -4, -2, -2, -7, -5, -6, -7,
            -5, -8, -2,  0, -1,-13, -8, -2, -3, -3, -3,-17 },
    /*R*/ { -7,  8, -6,-10, -8, -2, -9, -9, -2, -5, -8,  0,
            -4, -9, -4, -3, -6, -2,-10, -8, -7, -4, -6,-17 },
    /*N*/ { -4, -6,  8,  2,-11, -3, -2, -3,  0, -5, -7, -1,
            -9, -9, -6,  0, -2, -8, -4, -8,  6, -3, -3,-17 },
    /*D*/ { -3,-10,  2,  8,-14, -2,  2, -3, -4, -7,-12, -4,
           -11,-15, -8, -4, -5,-15,-11, -8,  6,  1, -5,-17 },
    /*C*/ { -6, -8,-11,-14, 10,-14,-14, -9, -7, -6,-15,-14,
           -13,-13, -8, -3, -8,-15, -4, -6,-12,-14, -9,-17 },
    /*Q*/ { -4, -2, -3, -2,-14,  8,  1, -7,  1, -8, -5, -3,
            -4,-13, -3, -5, -5,-13,-12, -7, -3,  6, -5,-17 },
    /*E*/ { -2, -9, -2,  2,-14,  1,  8, -4, -5, -5, -9, -4,
            -7,-14, -5, -4, -6,-17, -8, -6,  1,  6, -5,-17 },
    /*G*/ { -2, -9, -3, -3, -9, -7, -4,  6, -9,-11,-10, -7,
            -8, -9, -6, -2, -6,-15,-14, -5, -3, -5, -5,-17 },
    /*H*/ { -7, -2,  0, -4, -7,  1, -5, -9,  9, -9, -6, -6,
           -10, -6, -4, -6, -7, -7, -3, -6, -1, -1, -5,-17 },
    /*I*/ { -5, -5, -5, -7, -6, -8, -5,-11, -9,  8, -1, -6,
            -1, -2, -8, -7, -2,-14, -6,  2, -6, -6, -5,-17 },
    /*L*/ { -6, -8, -7,-12,-15, -5, -9,-10, -6, -1,  7, -8,
             1, -3, -7, -8, -7, -6, -7, -2, -9, -7, -6,-17 },
    /*K*/ { -7,  0, -1, -4,-14, -3, -4, -7, -6, -6, -8,  7,
            -2,-14, -6, -4, -3,-12, -9, -9, -2, -4, -5,-17 },
    /*M*/ { -5, -4, -9,-11,-13, -4, -7, -8,-10, -1,  1, -2,
            11, -4, -8, -5, -4,-13,-11, -1,-10, -5, -5,-17 },
    /*F*/ { -8, -9, -9,-15,-13,-13,-14, -9, -6, -2, -3,-14,
            -4,  9,-10, -6, -9, -4,  2, -8,-10,-13, -8,-17 },
    /*P*/ { -2, -4, -6, -8, -8, -3, -5, -6, -4, -8, -7, -6,
            -8,-10,  8, -2, -4,-14,-13, -6, -7, -4, -5,-17 },
    /*S*/ {  0, -3,  0, -4, -3, -5, -4, -2, -6, -7, -8, -4,
            -5, -6, -2,  6,  0, -5, -7, -6, -1, -5, -3,-17 },
    /*T*/ { -1, -6, -2, -5, -8, -5, -6, -6, -7, -2, -7, -3,
            -4, -9, -4,  0,  7,-13, -6, -3, -3, -6, -4,-17 },
    /*W*/ {-13, -2, -8,-15,-15,-13,-17,-15, -7,-14, -6,-12,
           -13, -4,-14, -5,-13, 13, -5,-15,-10,-14,-11,-17 },
    /*Y*/ { -8,-10, -4,-11, -4,-12, -8,-14, -3, -6, -7, -9,
           -11,  2,-13, -7, -6, -5, 10, -7, -6, -9, -7,-17 },
    /*V*/ { -2, -8, -8, -8, -6, -7, -6, -5, -6,  2, -2, -9,
            -1, -8, -6, -6, -3,-15, -7,  7, -8, -6, -5,-17 },
    /*B*/ { -3, -7,  6,  6,-12, -3,  1, -3, -1, -6, -9, -2,
           -10,-10, -7, -1, -3,-10, -6, -8,  6,  0, -5,-17 },
    /*Z*/ { -3, -4, -3,  1,-14,  6,  6, -5, -1, -6, -7, -4,
            -5,-13, -4, -5, -6,-14, -9, -6,  0,  6, -5,-17 },
    /*X*/ { -3, -6, -3, -5, -9, -5, -5, -5, -5, -5, -6, -5,
            -5, -8, -5, -3, -4,-11, -7, -5, -5, -5, -5,-17 },
    /***/ {-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,
           -17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,  1 }
};
const SNCBIPackedScoreMatrix NCBISM_Pam30 = {
    "ARNDCQEGHILKMFPSTWYVBZX*",
    s_Pam30PSM[0],
    -17
};