matrix_freq_ratios.c

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: matrix_freq_ratios.c,v $
 * PRODUCTION Revision 1000.0  2004/06/01 18:13:58  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

static char const rcsid[] =
    "$Id: matrix_freq_ratios.c,v 1000.0 2004/06/01 18:13:58 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
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 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Christiam Camacho
 *
 */

/** @file matrix_freq_ratios.c
 *  Definitions for various scoring matrices' frequency ratios.
 */
    
#include <algo/blast/core/blast_def.h>
#include "matrix_freq_ratios.h"
#include "blast_psi_priv.h"

/*underlying frequency ratios for BLOSUM62 as determined by Stephen Altschul;
  Stephen and Jorja Henikoff used different number for B,Z,X*/
static const double BLOSUM62_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE] = {
 {0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
  0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
  0.000, 0.000, 0.000, 0.250},
 {0.000, 3.903, 0.565, 0.868, 0.545, 0.741, 0.465, 1.057, 0.569, 0.632, 0.775,
  0.602, 0.723, 0.588, 0.754, 0.757, 0.613, 1.472, 0.984, 0.936, 0.416, 0.750,
  0.543, 0.747, 0.000, 0.250},
 {0.000, 0.565, 4.438, 0.345, 4.743, 1.335, 0.324, 0.739, 0.925, 0.334, 0.855,
  0.297, 0.405, 4.071, 0.554, 0.944, 0.703, 1.058, 0.826, 0.351, 0.253, 0.750,
  0.409, 1.184, 0.000, 0.250}, 
 {0.000, 0.868, 0.345, 19.577, 0.301, 0.286, 0.439, 0.420, 0.355, 0.653, 0.349,
  0.642, 0.611, 0.398, 0.380, 0.366, 0.309, 0.738, 0.741, 0.756, 0.450, 0.750,
  0.434, 0.317, 0.000, 0.250},
 {0.000, 0.545, 4.743, 0.301, 7.398, 1.688, 0.299, 0.634, 0.679, 0.339, 0.784,
  0.287, 0.346, 1.554, 0.599, 0.897, 0.573, 0.913, 0.695, 0.337, 0.232, 0.750,
  0.346, 1.382, 0.000, 0.250},
 {0.000, 0.741, 1.335, 0.286, 1.688, 5.470, 0.331, 0.481, 0.960, 0.331, 1.308,
  0.373, 0.500, 0.911, 0.679, 1.902, 0.961, 0.950, 0.741, 0.429, 0.374, 0.750,
  0.496, 4.090, 0.000, 0.250},
 {0.000, 0.465, 0.324, 0.439, 0.299, 0.331, 8.129, 0.341, 0.652, 0.946, 0.344,
  1.155, 1.004, 0.354, 0.287, 0.334, 0.381, 0.440, 0.482, 0.745, 1.374, 0.750,
  2.769, 0.332, 0.000, 0.250}, 
 {0.000, 1.057, 0.739, 0.420, 0.634, 0.481, 0.341, 6.876, 0.493, 0.275, 0.589,
  0.284, 0.396, 0.864, 0.477, 0.539, 0.450, 0.904, 0.579, 0.337, 0.422, 0.750,
  0.349, 0.503, 0.000, 0.250},
 {0.000, 0.569, 0.925, 0.355, 0.679, 0.960, 0.652, 0.493, 13.506, 0.326, 0.779,
  0.381, 0.584, 1.222, 0.473, 1.168, 0.917, 0.737, 0.557, 0.339, 0.444, 0.750,
  1.798, 1.040, 0.000, 0.250},
 {0.000, 0.632, 0.334, 0.653, 0.339, 0.331, 0.946, 0.275, 0.326, 3.998, 0.396,
  1.694, 1.478, 0.328, 0.385, 0.383, 0.355, 0.443, 0.780, 2.417, 0.409, 0.750,
  0.630, 0.351, 0.000, 0.250}, 
 {0.000, 0.775, 0.855, 0.349, 0.784, 1.308, 0.344, 0.589, 0.779, 0.396, 4.764,
  0.428, 0.625, 0.940, 0.704, 1.554, 2.077, 0.932, 0.793, 0.457, 0.359, 0.750,
  0.532, 1.403, 0.000, 0.250},
 {0.000, 0.602, 0.297, 0.642, 0.287, 0.373, 1.155, 0.284, 0.381, 1.694, 0.428,
  3.797, 1.994, 0.310, 0.371, 0.477, 0.474, 0.429, 0.660, 1.314, 0.568, 0.750,
  0.692, 0.413, 0.000, 0.250},
 {0.000, 0.723, 0.405, 0.611, 0.346, 0.500, 1.004, 0.396, 0.584, 1.478, 0.625,
  1.994, 6.481, 0.474, 0.424, 0.864, 0.623, 0.599, 0.794, 1.269, 0.610, 0.750,
  0.708, 0.641, 0.000, 0.250},
 {0.000, 0.588, 4.071, 0.398, 1.554, 0.911, 0.354, 0.864, 1.222, 0.328, 0.940,
  0.310, 0.474, 7.094, 0.500, 1.001, 0.859, 1.232, 0.984, 0.369, 0.278, 0.750,
  0.486, 0.946, 0.000, 0.250},
 {0.000, 0.754, 0.554, 0.380, 0.599, 0.679, 0.287, 0.477, 0.473, 0.385, 0.704,
  0.371, 0.424, 0.500, 12.838, 0.641, 0.481, 0.755, 0.689, 0.443, 0.282, 0.750,
  0.363, 0.664, 0.000, 0.250},
 {0.000, 0.757, 0.944, 0.366, 0.897, 1.902, 0.334, 0.539, 1.168, 0.383, 1.554,
  0.477, 0.864, 1.001, 0.641, 6.244, 1.406, 0.966, 0.791, 0.467, 0.509, 0.750,
  0.611, 3.582, 0.000, 0.250},
 {0.000, 0.613, 0.703, 0.309, 0.573, 0.961, 0.381, 0.450, 0.917, 0.355, 2.077,
  0.474, 0.623, 0.859, 0.481, 1.406, 6.666, 0.767, 0.678, 0.420, 0.395, 0.750,
  0.556, 1.133, 0.000, 0.250},
 {0.000, 1.472, 1.058, 0.738, 0.913, 0.950, 0.440, 0.904, 0.737, 0.443, 0.932,
  0.429, 0.599, 1.232, 0.755, 0.966, 0.767, 3.843, 1.614, 0.565, 0.385, 0.750,
  0.557, 0.956, 0.000, 0.250},
 {0.000, 0.984, 0.826, 0.741, 0.695, 0.741, 0.482, 0.579, 0.557, 0.780, 0.793,
  0.660, 0.794, 0.984, 0.689, 0.791, 0.678, 1.614, 4.832, 0.981, 0.431, 0.750,
  0.573, 0.761, 0.000, 0.250},
 {0.000, 0.936, 0.351, 0.756, 0.337, 0.429, 0.745, 0.337, 0.339, 2.417, 0.457,
  1.314, 1.269, 0.369, 0.443, 0.467, 0.420, 0.565, 0.981, 3.692, 0.374, 0.750,
  0.658, 0.444, 0.000, 0.250},
 {0.000, 0.416, 0.253, 0.450, 0.232, 0.374, 1.374, 0.422, 0.444, 0.409, 0.359,
  0.568, 0.610, 0.278, 0.282, 0.509, 0.395, 0.385, 0.431, 0.374, 38.108, 0.750,
  2.110, 0.426, 0.000, 0.250},
 {0.000, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750,
  0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750,
  0.750, 0.750, 0.000, 0.250},
 {0.000, 0.543, 0.409, 0.434, 0.346, 0.496, 2.769, 0.349, 1.798, 0.630, 0.532,
  0.692, 0.708, 0.486, 0.363, 0.611, 0.556, 0.557, 0.573, 0.658, 2.110, 0.750,
  9.832, 0.541, 0.000, 0.250},
 {0.000, 0.747, 1.184, 0.317, 1.382, 4.090, 0.332, 0.503, 1.040, 0.351, 1.403,
  0.413, 0.641, 0.946, 0.664, 3.582, 1.133, 0.956, 0.761, 0.444, 0.426, 0.750,
  0.541, 3.893, 0.000, 0.250},
 {0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
  0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
  0.000, 0.000, 0.000, 0.250}, 
 {0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250,
  0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250, 0.250,
  0.250, 0.250, 0.250, 1.333}, 
};

static const double PAM30_FREQRATIOS[BLASTAA_SIZE][BLASTAA_SIZE] = {
{0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.003},
{0.000, 7.789, 0.302, 0.108, 0.317, 0.453, 0.057, 0.576, 0.083, 0.199, 0.095, 0.115, 0.189, 0.285, 0.593, 0.235, 0.091, 0.875, 0.827, 0.477, 0.010, 0.750, 0.070, 0.358, 0.000, 0.003},
{0.000, 0.302, 8.118, 0.015, 8.456, 1.472, 0.027, 0.338, 0.664, 0.126, 0.441, 0.049, 0.034, 7.726, 0.102, 0.368, 0.082, 0.604, 0.353, 0.067, 0.032, 0.750, 0.114, 0.991, 0.000, 0.003},
{0.000, 0.108, 0.015, 27.591, 0.008, 0.008, 0.012, 0.042, 0.078, 0.119, 0.008, 0.006, 0.009, 0.024, 0.063, 0.008, 0.068, 0.379, 0.068, 0.132, 0.005, 0.750, 0.258, 0.008, 0.000, 0.003},
{0.000, 0.317, 8.456, 0.008, 14.236, 2.342, 0.006, 0.326, 0.271, 0.080, 0.220, 0.014, 0.023, 1.756, 0.068, 0.427, 0.029, 0.286, 0.200, 0.065, 0.005, 0.750, 0.020, 1.508, 0.000, 0.003},
{0.000, 0.453, 1.472, 0.008, 2.343, 13.663, 0.008, 0.232, 0.181, 0.150, 0.226, 0.043, 0.092, 0.464, 0.153, 1.507, 0.043, 0.226, 0.130, 0.110, 0.003, 0.750, 0.057, 8.365, 0.000, 0.003},
{0.000, 0.057, 0.027, 0.012, 0.006, 0.008, 21.408, 0.044, 0.132, 0.473, 0.009, 0.416, 0.250, 0.051, 0.036, 0.011, 0.042, 0.114, 0.051, 0.067, 0.213, 0.750, 1.786, 0.009, 0.000, 0.003},
{0.000, 0.576, 0.338, 0.042, 0.326, 0.232, 0.044, 9.314, 0.048, 0.024, 0.086, 0.028, 0.057, 0.351, 0.122, 0.094, 0.040, 0.553, 0.135, 0.149, 0.006, 0.750, 0.009, 0.172, 0.000, 0.003},
{0.000, 0.083, 0.664, 0.078, 0.271, 0.181, 0.132, 0.048, 22.927, 0.044, 0.120, 0.123, 0.028, 1.119, 0.248, 1.359, 0.587, 0.132, 0.086, 0.115, 0.081, 0.750, 0.324, 0.695, 0.000, 0.003},
{0.000, 0.199, 0.126, 0.119, 0.080, 0.150, 0.473, 0.024, 0.044, 18.632, 0.127, 0.643, 0.793, 0.179, 0.053, 0.070, 0.159, 0.097, 0.444, 1.938, 0.009, 0.750, 0.119, 0.115, 0.000, 0.003},
{0.000, 0.095, 0.441, 0.008, 0.220, 0.226, 0.009, 0.086, 0.120, 0.127, 9.988, 0.061, 0.563, 0.697, 0.106, 0.384, 1.111, 0.260, 0.336, 0.046, 0.018, 0.750, 0.042, 0.295, 0.000, 0.003},
{0.000, 0.115, 0.049, 0.006, 0.014, 0.043, 0.416, 0.028, 0.123, 0.643, 0.061, 10.019, 1.242, 0.090, 0.090, 0.185, 0.053, 0.058, 0.103, 0.463, 0.127, 0.750, 0.095, 0.105, 0.000, 0.003},
{0.000, 0.189, 0.034, 0.009, 0.023, 0.092, 0.250, 0.057, 0.028, 0.792, 0.563, 1.242, 46.604, 0.047, 0.065, 0.272, 0.243, 0.161, 0.263, 0.631, 0.013, 0.750, 0.021, 0.171, 0.000, 0.003},
{0.000, 0.285, 7.726, 0.024, 1.756, 0.464, 0.051, 0.351, 1.119, 0.179, 0.697, 0.090, 0.047, 14.647, 0.142, 0.299, 0.144, 0.972, 0.531, 0.070, 0.064, 0.750, 0.223, 0.392, 0.000, 0.003},
{0.000, 0.593, 0.102, 0.063, 0.068, 0.153, 0.036, 0.122, 0.248, 0.053, 0.106, 0.090, 0.065, 0.142, 15.809, 0.376, 0.270, 0.571, 0.240, 0.140, 0.009, 0.750, 0.010, 0.251, 0.000, 0.003},
{0.000, 0.235, 0.368, 0.008, 0.427, 1.507, 0.011, 0.094, 1.360, 0.070, 0.384, 0.185, 0.272, 0.299, 0.376, 18.136, 0.585, 0.168, 0.150, 0.103, 0.012, 0.750, 0.017, 8.754, 0.000, 0.003},
{0.000, 0.091, 0.082, 0.068, 0.029, 0.043, 0.042, 0.040, 0.587, 0.159, 1.111, 0.053, 0.243, 0.144, 0.270, 0.585, 18.926, 0.355, 0.106, 0.074, 0.517, 0.750, 0.030, 0.279, 0.000, 0.003},
{0.000, 0.875, 0.604, 0.379, 0.286, 0.226, 0.114, 0.553, 0.132, 0.097, 0.260, 0.058, 0.161, 0.972, 0.571, 0.168, 0.355, 9.028, 1.145, 0.118, 0.179, 0.750, 0.097, 0.200, 0.000, 0.003},
{0.000, 0.827, 0.353, 0.068, 0.200, 0.130, 0.051, 0.135, 0.086, 0.444, 0.336, 0.103, 0.263, 0.531, 0.240, 0.150, 0.106, 1.145, 11.695, 0.391, 0.013, 0.750, 0.112, 0.139, 0.000, 0.003},
{0.000, 0.477, 0.067, 0.132, 0.065, 0.110, 0.067, 0.149, 0.115, 1.938, 0.046, 0.463, 0.631, 0.070, 0.141, 0.103, 0.074, 0.118, 0.391, 11.609, 0.005, 0.750, 0.081, 0.107, 0.000, 0.003},
{0.000, 0.010, 0.032, 0.005, 0.005, 0.003, 0.213, 0.006, 0.081, 0.009, 0.018, 0.127, 0.013, 0.064, 0.009, 0.012, 0.517, 0.179, 0.013, 0.005, 88.722, 0.750, 0.173, 0.007, 0.000, 0.003},
{0.000, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.750, 0.000, 0.003},
{0.000, 0.070, 0.114, 0.258, 0.020, 0.057, 1.786, 0.009, 0.324, 0.119, 0.042, 0.095, 0.021, 0.223, 0.010, 0.017, 0.030, 0.097, 0.112, 0.081, 0.173, 0.750, 28.442, 0.039, 0.000, 0.003},
{0.000, 0.358, 0.991, 0.008, 1.508, 8.365, 0.009, 0.172, 0.695, 0.115, 0.295, 0.105, 0.171, 0.392, 0.251, 8.754, 0.279, 0.200, 0.139, 0.107, 0.007, 0.750, 0.039, 8.535, 0.000, 0.003},