msa
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358
Sonali Arora authored on 10/04/2015 00:12:33 | 1 | 1 |
new file mode 100644 |
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+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
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+ |
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+/********************************************************************* |
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+ * Clustal Omega - Multiple sequence alignment |
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+ * |
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+ * Copyright (C) 2010 University College Dublin |
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+ * |
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+ * Clustal-Omega is free software; you can redistribute it and/or |
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+ * modify it under the terms of the GNU General Public License as |
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+ * published by the Free Software Foundation; either version 2 of the |
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+ * License, or (at your option) any later version. |
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+ * |
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+ * This file is part of Clustal-Omega. |
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+ * |
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+ ********************************************************************/ |
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+ |
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+/* |
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+ * RCS $Id: hhmatrices-C.h 274 2012-04-24 23:28:24Z dave $ |
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+ */ |
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+ |
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+// Substitution matrices and their background frequencies |
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+ |
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+// The following background frequencies were calculated by the formula pa = (P[a,b]/(pa*pb))^(-1) * (1,...,1) |
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+// For the Blousum50-matrix this becomes pb[a]= SUM_(b=1,20) (2^(BLOSUM50[a,b]/3))^(-1) |
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+// A R N D C Q E G H I L K M F P S T W Y V |
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+// Gonnet 7.68,5.14,4.02,5.41,1.89,3.27,5.99,7.56,3.69,5.06,10.01,5.97,2.20,3.50,4.54,4.67,7.12,1.25,3.95,7.28 |
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+// BLOSUM50 8.24,6.24,4.46,4.77,2.03,2.90,6.78,6.69,2.53,6.89,10.7 ,5.04,1.49,4.93,3.97,5.95,6.13,1.34,3.45,6.28 |
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+ |
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+const float Gonnet[]={
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+// A R N D C Q E G H I L K M F P S T W Y V |
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+ 10227, 3430, 2875, 3869, 1625, 2393, 4590, 6500, 2352, 3225, 5819, 4172, 1435, 1579, 3728, 4610, 6264, 418, 1824, 5709, // A |
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+ 3430, 7780, 2209, 2589, 584, 2369, 3368, 3080, 2173, 1493, 3093, 5701, 763, 859, 1893, 2287, 3487, 444, 1338, 2356, // R |
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+ 2875, 2209, 3868, 3601, 501, 1541, 2956, 3325, 1951, 1065, 2012, 2879, 532, 688, 1480, 2304, 3204, 219, 1148, 1759, // N |
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+ 3869, 2589, 3601, 8618, 488, 2172, 6021, 4176, 2184, 1139, 2151, 3616, 595, 670, 2086, 2828, 3843, 204, 1119, 2015, // D |
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+ 1625, 584, 501, 488, 5034, 355, 566, 900, 516, 741, 1336, 591, 337, 549, 419, 901, 1197, 187, 664, 1373, // C |
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+ 2393, 2369, 1541, 2172, 355, 1987, 2891, 1959, 1587, 1066, 2260, 2751, 570, 628, 1415, 1595, 2323, 219, 871, 1682, // Q |
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+ 4590, 3368, 2956, 6021, 566, 2891, 8201, 3758, 2418, 1624, 3140, 4704, 830, 852, 2418, 2923, 4159, 278, 1268, 2809, // E |
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+ 6500, 3080, 3325, 4176, 900, 1959, 3758,26066, 2016, 1354, 2741, 3496, 741, 797, 2369, 3863, 4169, 375, 1186, 2569, // G |
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+ 2352, 2173, 1951, 2184, 516, 1587, 2418, 2016, 5409, 1123, 2380, 2524, 600, 1259, 1298, 1642, 2446, 383, 876, 1691, // H |
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+ 3225, 1493, 1065, 1139, 741, 1066, 1624, 1354, 1123, 6417, 9630, 1858, 1975, 2225, 1260, 1558, 3131, 417, 1697, 7504, // I |
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+ 5819, 3093, 2012, 2151, 1336, 2260, 3140, 2741, 2380, 9630,25113, 3677, 4187, 5540, 2670, 2876, 5272, 1063, 3945,11005, // L |
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+ 4172, 5701, 2879, 3616, 591, 2751, 4704, 3496, 2524, 1858, 3677, 7430, 949, 975, 2355, 2847, 4340, 333, 1451, 2932, // K |
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+ 1435, 763, 532, 595, 337, 570, 830, 741, 600, 1975, 4187, 949, 1300, 1111, 573, 743, 1361, 218, 828, 2310, // M |
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+ 1579, 859, 688, 670, 549, 628, 852, 797, 1259, 2225, 5540, 975, 1111, 6126, 661, 856, 1498, 1000, 4464, 2602, // F |
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+ 3728, 1893, 1480, 2086, 419, 1415, 2418, 2369, 1298, 1260, 2670, 2355, 573, 661,11834, 2320, 3300, 179, 876, 2179, // P |
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+ 4610, 2287, 2304, 2828, 901, 1595, 2923, 3863, 1642, 1558, 2876, 2847, 743, 856, 2320, 3611, 4686, 272, 1188, 2695, // S |
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+ 6264, 3487, 3204, 3843, 1197, 2323, 4159, 4169, 2446, 3131, 5272, 4340, 1361, 1498, 3300, 4686, 8995, 397, 1812, 5172, // T |
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+ 418, 444, 219, 204, 187, 219, 278, 375, 383, 417, 1063, 333, 218, 1000, 179, 272, 397, 4101, 1266, 499, // W |
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+ 1824, 1338, 1148, 1119, 664, 871, 1268, 1186, 876, 1697, 3945, 1451, 828, 4464, 876, 1188, 1812, 1266, 9380, 2227, // Y |
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+ 5709, 2356, 1759, 2015, 1373, 1682, 2809, 2569, 1691, 7504,11005, 2932, 2310, 2602, 2179, 2695, 5172, 499, 2227,11569};// V |
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+ |
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+const float Blosum30[]= {
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+// A R N D C Q E G H I L K M F P S T W Y V |
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+ 0.0096, |
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+ 0.0038,0.0109, |
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| 56 |
+ 0.0031,0.0019,0.0055, |
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+ 0.0043,0.0026,0.0027,0.0095, |
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| 58 |
+ 0.0014,0.0011,0.0010,0.0010,0.0070, |
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| 59 |
+ 0.0031,0.0031,0.0014,0.0018,0.0007,0.0039, |
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| 60 |
+ 0.0044,0.0031,0.0024,0.0037,0.0018,0.0028,0.0094, |
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| 61 |
+ 0.0052,0.0032,0.0032,0.0035,0.0011,0.0020,0.0035,0.0173, |
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| 62 |
+ 0.0016,0.0014,0.0011,0.0011,0.0004,0.0010,0.0018,0.0015,0.0060, |
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| 63 |
+ 0.0040,0.0022,0.0024,0.0018,0.0012,0.0016,0.0023,0.0036,0.0012,0.0072, |
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| 64 |
+ 0.0056,0.0039,0.0032,0.0043,0.0023,0.0027,0.0051,0.0051,0.0022,0.0066,0.0139, |
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| 65 |
+ 0.0044,0.0043,0.0027,0.0032,0.0010,0.0021,0.0053,0.0039,0.0013,0.0026,0.0044,0.0063, |
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| 66 |
+ 0.0018,0.0012,0.0009,0.0008,0.0004,0.0007,0.0012,0.0013,0.0008,0.0014,0.0027,0.0017,0.0012, |
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+ 0.0027,0.0023,0.0017,0.0011,0.0008,0.0010,0.0016,0.0022,0.0008,0.0027,0.0055,0.0023,0.0008,0.0077, |
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+ 0.0028,0.0021,0.0012,0.0021,0.0007,0.0015,0.0030,0.0030,0.0014,0.0017,0.0027,0.0029,0.0005,0.0011,0.0091, |
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+ 0.0056,0.0035,0.0028,0.0034,0.0013,0.0021,0.0038,0.0051,0.0017,0.0033,0.0047,0.0042,0.0010,0.0027,0.0024,0.0075, |
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+ 0.0040,0.0019,0.0024,0.0024,0.0009,0.0016,0.0023,0.0028,0.0010,0.0027,0.0046,0.0025,0.0010,0.0016,0.0020,0.0041,0.0046, |
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+ 0.0005,0.0007,0.0002,0.0004,0.0003,0.0004,0.0007,0.0011,0.0002,0.0005,0.0009,0.0006,0.0002,0.0007,0.0004,0.0005,0.0003,0.0027, |
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+ 0.0014,0.0022,0.0008,0.0015,0.0004,0.0011,0.0016,0.0016,0.0010,0.0018,0.0045,0.0017,0.0007,0.0024,0.0011,0.0017,0.0014,0.0009,0.0044, |
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+ 0.0056,0.0031,0.0022,0.0027,0.0012,0.0015,0.0026,0.0033,0.0012,0.0063,0.0074,0.0030,0.0015,0.0032,0.0017,0.0036,0.0036,0.0005,0.0024,0.0083}; |
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+ |
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+const float Blosum40[]= {
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+// A R N D C Q E G H I L K M F P S T W Y V |
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+ 0.0148, |
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+ 0.0029,0.0109, |
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+ 0.0029,0.0019,0.0069, |
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| 80 |
+ 0.0032,0.0021,0.0031,0.0126, |
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+ 0.0015,0.0007,0.0007,0.0009,0.0093, |
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+ 0.0026,0.0024,0.0017,0.0016,0.0004,0.0048, |
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| 83 |
+ 0.0040,0.0026,0.0023,0.0048,0.0010,0.0032,0.0118, |
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| 84 |
+ 0.0066,0.0023,0.0035,0.0031,0.0012,0.0020,0.0028,0.0260, |
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| 85 |
+ 0.0014,0.0012,0.0013,0.0014,0.0003,0.0010,0.0015,0.0014,0.0060, |
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| 86 |
+ 0.0037,0.0017,0.0017,0.0016,0.0008,0.0012,0.0018,0.0024,0.0009,0.0105, |
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| 87 |
+ 0.0050,0.0030,0.0021,0.0027,0.0015,0.0023,0.0036,0.0034,0.0017,0.0082,0.0209, |
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| 88 |
+ 0.0041,0.0051,0.0027,0.0030,0.0010,0.0026,0.0045,0.0035,0.0013,0.0023,0.0037,0.0099, |
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| 89 |
+ 0.0017,0.0010,0.0007,0.0007,0.0003,0.0007,0.0010,0.0013,0.0007,0.0018,0.0037,0.0012,0.0018, |
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| 90 |
+ 0.0022,0.0016,0.0013,0.0013,0.0008,0.0008,0.0015,0.0021,0.0009,0.0031,0.0055,0.0018,0.0011,0.0105, |
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+ 0.0027,0.0014,0.0014,0.0019,0.0005,0.0013,0.0026,0.0028,0.0008,0.0020,0.0021,0.0023,0.0007,0.0010,0.0151, |
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+ 0.0060,0.0025,0.0030,0.0030,0.0013,0.0026,0.0034,0.0052,0.0013,0.0025,0.0034,0.0034,0.0011,0.0019,0.0022,0.0089, |
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+ 0.0040,0.0019,0.0022,0.0024,0.0011,0.0015,0.0025,0.0029,0.0009,0.0028,0.0039,0.0029,0.0011,0.0019,0.0022,0.0043,0.0070, |
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+ 0.0007,0.0005,0.0003,0.0003,0.0001,0.0004,0.0005,0.0008,0.0002,0.0005,0.0009,0.0005,0.0002,0.0008,0.0003,0.0004,0.0003,0.0045, |
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+ 0.0019,0.0016,0.0010,0.0011,0.0004,0.0010,0.0014,0.0017,0.0012,0.0020,0.0031,0.0017,0.0010,0.0032,0.0009,0.0015,0.0014,0.0008,0.0060, |
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| 96 |
+ 0.0054,0.0023,0.0017,0.0022,0.0012,0.0014,0.0025,0.0028,0.0008,0.0083,0.0082,0.0027,0.0018,0.0031,0.0018,0.0032,0.0040,0.0005,0.0020,0.0113}; |
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+ |
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+const float Blosum50[]= {
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+// A R N D C Q E G H I L K M F P S T W Y V |
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+ 0.0192, |
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| 101 |
+ 0.0027,0.0152, |
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| 102 |
+ 0.0024,0.0020,0.0101, |
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| 103 |
+ 0.0026,0.0019,0.0035,0.0161, |
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| 104 |
+ 0.0015,0.0005,0.0006,0.0005,0.0091, |
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| 105 |
+ 0.0022,0.0025,0.0016,0.0017,0.0004,0.0057, |
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| 106 |
+ 0.0034,0.0029,0.0023,0.0048,0.0006,0.0033,0.0141, |
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| 107 |
+ 0.0062,0.0020,0.0031,0.0028,0.0009,0.0017,0.0023,0.0316, |
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| 108 |
+ 0.0012,0.0013,0.0015,0.0011,0.0003,0.0010,0.0013,0.0011,0.0064, |
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| 109 |
+ 0.0035,0.0015,0.0013,0.0012,0.0008,0.0011,0.0015,0.0018,0.0007,0.0140, |
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| 110 |
+ 0.0048,0.0028,0.0017,0.0018,0.0014,0.0019,0.0026,0.0027,0.0013,0.0104,0.0304, |
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| 111 |
+ 0.0033,0.0064,0.0027,0.0026,0.0006,0.0029,0.0043,0.0028,0.0014,0.0017,0.0027,0.0130, |
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| 112 |
+ 0.0016,0.0009,0.0007,0.0005,0.0004,0.0008,0.0008,0.0009,0.0005,0.0022,0.0042,0.0010,0.0029, |
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| 113 |
+ 0.0020,0.0012,0.0009,0.0008,0.0006,0.0007,0.0012,0.0015,0.0009,0.0030,0.0058,0.0012,0.0012,0.0154, |
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| 114 |
+ 0.0022,0.0011,0.0011,0.0015,0.0004,0.0011,0.0019,0.0019,0.0006,0.0013,0.0017,0.0018,0.0005,0.0007,0.0171, |
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| 115 |
+ 0.0062,0.0025,0.0032,0.0028,0.0011,0.0022,0.0030,0.0044,0.0012,0.0021,0.0029,0.0031,0.0010,0.0016,0.0018,0.0111, |
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| 116 |
+ 0.0039,0.0021,0.0026,0.0022,0.0010,0.0015,0.0024,0.0025,0.0009,0.0029,0.0038,0.0026,0.0011,0.0015,0.0016,0.0047,0.0100, |
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| 117 |
+ 0.0005,0.0004,0.0002,0.0002,0.0001,0.0003,0.0004,0.0005,0.0002,0.0005,0.0008,0.0004,0.0003,0.0009,0.0002,0.0003,0.0004,0.0059, |
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| 118 |
+ 0.0015,0.0013,0.0009,0.0009,0.0004,0.0009,0.0012,0.0012,0.0013,0.0018,0.0027,0.0013,0.0007,0.0039,0.0006,0.0013,0.0012,0.0008,0.0077, |
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| 119 |
+ 0.0054,0.0020,0.0015,0.0016,0.0013,0.0014,0.0020,0.0022,0.0007,0.0107,0.0092,0.0022,0.0021,0.0030,0.0016,0.0029,0.0041,0.0005,0.0018,0.0164}; |
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| 120 |
+ |
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| 121 |
+const float Blosum65[]= {
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| 122 |
+// A R N D C Q E G H I L K M F P S T W Y V |
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| 123 |
+ 0.0222, |
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| 124 |
+ 0.0022,0.0181, |
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| 125 |
+ 0.0019,0.0019,0.0148, |
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| 126 |
+ 0.0021,0.0015,0.0037,0.0225, |
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| 127 |
+ 0.0016,0.0004,0.0004,0.0004,0.0127, |
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| 128 |
+ 0.0018,0.0024,0.0015,0.0016,0.0003,0.0076, |
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| 129 |
+ 0.0029,0.0025,0.0021,0.0049,0.0003,0.0034,0.0168, |
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| 130 |
+ 0.0057,0.0016,0.0027,0.0024,0.0007,0.0013,0.0018,0.0396, |
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| 131 |
+ 0.0010,0.0013,0.0014,0.0009,0.0002,0.0010,0.0013,0.0009,0.0096, |
|
| 132 |
+ 0.0031,0.0012,0.0009,0.0011,0.0012,0.0008,0.0012,0.0013,0.0006,0.0191, |
|
| 133 |
+ 0.0043,0.0023,0.0013,0.0014,0.0016,0.0016,0.0019,0.0020,0.0009,0.0115,0.0388, |
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| 134 |
+ 0.0032,0.0062,0.0024,0.0024,0.0005,0.0030,0.0040,0.0024,0.0012,0.0015,0.0024,0.0166, |
|
| 135 |
+ 0.0013,0.0007,0.0005,0.0004,0.0004,0.0007,0.0006,0.0007,0.0003,0.0025,0.0052,0.0008,0.0045, |
|
| 136 |
+ 0.0016,0.0009,0.0007,0.0007,0.0005,0.0005,0.0008,0.0011,0.0008,0.0030,0.0056,0.0009,0.0012,0.0186, |
|
| 137 |
+ 0.0021,0.0009,0.0008,0.0011,0.0003,0.0008,0.0014,0.0013,0.0005,0.0009,0.0013,0.0015,0.0004,0.0005,0.0195, |
|
| 138 |
+ 0.0065,0.0022,0.0030,0.0027,0.0011,0.0018,0.0029,0.0037,0.0011,0.0017,0.0024,0.0030,0.0008,0.0012,0.0016,0.0137, |
|
| 139 |
+ 0.0037,0.0017,0.0022,0.0019,0.0009,0.0013,0.0021,0.0022,0.0007,0.0027,0.0033,0.0023,0.0010,0.0012,0.0013,0.0048,0.0133, |
|
| 140 |
+ 0.0004,0.0003,0.0002,0.0001,0.0002,0.0002,0.0002,0.0004,0.0002,0.0004,0.0007,0.0003,0.0002,0.0009,0.0001,0.0003,0.0003,0.0074, |
|
| 141 |
+ 0.0013,0.0009,0.0007,0.0006,0.0004,0.0006,0.0008,0.0008,0.0016,0.0015,0.0023,0.0010,0.0006,0.0043,0.0004,0.0010,0.0009,0.0010,0.0113, |
|
| 142 |
+ 0.0049,0.0015,0.0011,0.0012,0.0014,0.0011,0.0016,0.0017,0.0006,0.0120,0.0094,0.0019,0.0023,0.0025,0.0012,0.0023,0.0035,0.0004,0.0015,0.0206}; |
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| 143 |
+ |
|
| 144 |
+ |
|
| 145 |
+const float Blosum80[]= {
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|
| 146 |
+// A R N D C Q E G H I L K M F P S T W Y V |
|
| 147 |
+ 0.0252, |
|
| 148 |
+ 0.0020,0.0210, |
|
| 149 |
+ 0.0016,0.0017,0.0166, |
|
| 150 |
+ 0.0018,0.0013,0.0037,0.0262, |
|
| 151 |
+ 0.0015,0.0003,0.0004,0.0003,0.0172, |
|
| 152 |
+ 0.0017,0.0024,0.0014,0.0014,0.0003,0.0094, |
|
| 153 |
+ 0.0028,0.0023,0.0019,0.0048,0.0003,0.0035,0.0208, |
|
| 154 |
+ 0.0053,0.0015,0.0025,0.0022,0.0006,0.0011,0.0017,0.0463, |
|
| 155 |
+ 0.0009,0.0012,0.0012,0.0008,0.0002,0.0011,0.0012,0.0008,0.0104, |
|
| 156 |
+ 0.0027,0.0010,0.0007,0.0008,0.0011,0.0007,0.0010,0.0009,0.0004,0.0220, |
|
| 157 |
+ 0.0036,0.0018,0.0011,0.0011,0.0014,0.0014,0.0015,0.0016,0.0008,0.0111,0.0442, |
|
| 158 |
+ 0.0029,0.0061,0.0022,0.0020,0.0004,0.0028,0.0036,0.0020,0.0010,0.0012,0.0019,0.0190, |
|
| 159 |
+ 0.0011,0.0006,0.0004,0.0003,0.0004,0.0007,0.0006,0.0005,0.0003,0.0025,0.0052,0.0007,0.0053, |
|
| 160 |
+ 0.0014,0.0007,0.0006,0.0006,0.0005,0.0005,0.0006,0.0009,0.0007,0.0027,0.0052,0.0007,0.0010,0.0211, |
|
| 161 |
+ 0.0021,0.0009,0.0007,0.0009,0.0003,0.0007,0.0012,0.0010,0.0004,0.0007,0.0012,0.0012,0.0003,0.0004,0.0221, |
|
| 162 |
+ 0.0064,0.0020,0.0029,0.0024,0.0010,0.0017,0.0026,0.0034,0.0010,0.0015,0.0021,0.0026,0.0007,0.0010,0.0014,0.0167, |
|
| 163 |
+ 0.0036,0.0015,0.0020,0.0016,0.0009,0.0012,0.0019,0.0019,0.0007,0.0024,0.0028,0.0020,0.0009,0.0011,0.0011,0.0048,0.0156, |
|
| 164 |
+ 0.0003,0.0002,0.0001,0.0001,0.0001,0.0002,0.0002,0.0003,0.0001,0.0003,0.0006,0.0002,0.0002,0.0007,0.0001,0.0002,0.0002,0.0087, |
|
| 165 |
+ 0.0011,0.0007,0.0006,0.0005,0.0003,0.0005,0.0006,0.0006,0.0016,0.0013,0.0020,0.0008,0.0005,0.0046,0.0003,0.0009,0.0008,0.0010,0.0148, |
|
| 166 |
+ 0.0046,0.0013,0.0009,0.0010,0.0013,0.0010,0.0015,0.0014,0.0005,0.0123,0.0089,0.0015,0.0022,0.0022,0.0010,0.0021,0.0033,0.0004,0.0012,0.0246}; |
|
| 167 |
+ |
|
| 168 |
+const float mism = 2000; // standard mismatch score |
|
| 169 |
+const float matc = 7000; |
|
| 170 |
+ |
|
| 171 |
+// RNA matrix, Gonnet type format |
|
| 172 |
+const float ribosum[]={
|
|
| 173 |
+// A C G T U R Y M K S W B D H V N ? ? ? ? |
|
| 174 |
+ 9500, 600, 700, 900, 900, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A |
|
| 175 |
+ 600, 4000, 300, 1200, 1200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C |
|
| 176 |
+ 700, 300, 3500, 700, 700, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G |
|
| 177 |
+ 900, 1200, 700, 8200, 8200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T |
|
| 178 |
+ 900, 1200, 700, 8200, 8200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U |
|
| 179 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R |
|
| 180 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y |
|
| 181 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M |
|
| 182 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K |
|
| 183 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S |
|
| 184 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W |
|
| 185 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B |
|
| 186 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D |
|
| 187 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H |
|
| 188 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V |
|
| 189 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N |
|
| 190 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 191 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 192 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 193 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ? |
|
| 194 |
+ |
|
| 195 |
+const float dna_basic[]={
|
|
| 196 |
+// A C G T U R Y M K S W B D H V N ? ? ? ? |
|
| 197 |
+ matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A |
|
| 198 |
+ mism, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C |
|
| 199 |
+ mism, mism, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G |
|
| 200 |
+ mism, mism, mism, matc, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T |
|
| 201 |
+ mism, mism, mism, matc, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U |
|
| 202 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R |
|
| 203 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y |
|
| 204 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M |
|
| 205 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K |
|
| 206 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S |
|
| 207 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W |
|
| 208 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B |
|
| 209 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D |
|
| 210 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H |
|
| 211 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V |
|
| 212 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N |
|
| 213 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 214 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 215 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 216 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ? |
|
| 217 |
+ |
|
| 218 |
+const float dave_nucleo[]={
|
|
| 219 |
+// A C G T U R Y M K S W B D H V N ? ? ? ? |
|
| 220 |
+ 8000, 1500, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A |
|
| 221 |
+ 1500, 6500, 1000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C |
|
| 222 |
+ mism, 1000, 6500, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G |
|
| 223 |
+ mism, mism, mism, 7000, 7000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T |
|
| 224 |
+ mism, mism, mism, 7000, 7000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U |
|
| 225 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R |
|
| 226 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y |
|
| 227 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M |
|
| 228 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K |
|
| 229 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S |
|
| 230 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W |
|
| 231 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B |
|
| 232 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D |
|
| 233 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H |
|
| 234 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V |
|
| 235 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N |
|
| 236 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 237 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 238 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ? |
|
| 239 |
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ? |
|
| 240 |
+ |
|
| 241 |
+// prediction accuracy of Psipred: |
|
| 242 |
+// Ppred[cf][B][A] = P(A,B,cf)/P(A)/P(B,cf) = P(A|B,cf)/P(A) |
|
| 243 |
+// A = observed ss state B = predicted ss state cf = confidence value of prediction |
|
| 244 |
+//float Ppred[MAXCF][NSSPRED][NDSSP]= |
|
| 245 |
+const float Ppred[]= |
|
| 246 |
+ {
|
|
| 247 |
+//pred/obs - H E ~ S T G B |
|
| 248 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=- |
|
| 249 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // H |
|
| 250 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // E |
|
| 251 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // ~ |
|
| 252 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=0 |
|
| 253 |
+ 1.000, 1.128, 0.519, 0.834, 0.957, 1.488, 2.106, 1.085 , // H |
|
| 254 |
+ 1.000, 0.233, 2.240, 1.216, 0.913, 0.519, 0.923, 1.759 , // E |
|
| 255 |
+ 1.000, 0.640, 1.017, 1.122, 1.069, 1.242, 2.140, 1.999 , // ~ |
|
| 256 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=1 |
|
| 257 |
+ 1.000, 1.251, 0.485, 0.771, 0.847, 1.371, 2.266, 0.864 , // H |
|
| 258 |
+ 1.000, 0.222, 2.542, 1.069, 0.804, 0.428, 0.671, 1.728 , // E |
|
| 259 |
+ 1.000, 0.474, 1.103, 1.295, 1.232, 1.214, 1.835, 1.989 , // ~ |
|
| 260 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=2 |
|
| 261 |
+ 1.000, 1.383, 0.426, 0.637, 0.778, 1.349, 2.436, 0.824 , // H |
|
| 262 |
+ 1.000, 0.202, 2.769, 0.999, 0.714, 0.320, 0.551, 1.566 , // E |
|
| 263 |
+ 1.000, 0.395, 1.005, 1.407, 1.376, 1.336, 1.725, 2.063 , // ~ |
|
| 264 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=3 |
|
| 265 |
+ 1.000, 1.531, 0.369, 0.552, 0.682, 1.280, 2.420, 0.698 , // H |
|
| 266 |
+ 1.000, 0.169, 2.970, 0.954, 0.556, 0.273, 0.489, 1.504 , // E |
|
| 267 |
+ 1.000, 0.352, 0.843, 1.515, 1.542, 1.456, 1.684, 1.958 , // ~ |
|
| 268 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=4 |
|
| 269 |
+ 1.000, 1.750, 0.305, 0.444, 0.537, 1.134, 2.295, 0.600 , // H |
|
| 270 |
+ 1.000, 0.124, 3.179, 0.847, 0.513, 0.228, 0.413, 1.897 , // E |
|
| 271 |
+ 1.000, 0.282, 0.718, 1.664, 1.630, 1.577, 1.625, 1.877 , // ~ |
|
| 272 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=5 |
|
| 273 |
+ 1.000, 1.952, 0.250, 0.353, 0.456, 0.982, 2.050, 0.466 , // H |
|
| 274 |
+ 1.000, 0.102, 3.464, 0.699, 0.453, 0.174, 0.284, 1.357 , // E |
|
| 275 |
+ 1.000, 0.227, 0.574, 1.782, 1.846, 1.681, 1.418, 1.885 , // ~ |
|
| 276 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=6 |
|
| 277 |
+ 1.000, 2.183, 0.171, 0.263, 0.319, 0.792, 1.933, 0.345 , // H |
|
| 278 |
+ 1.000, 0.079, 3.712, 0.612, 0.281, 0.133, 0.196, 1.089 , // E |
|
| 279 |
+ 1.000, 0.173, 0.458, 1.915, 2.007, 1.766, 1.220, 1.704 , // ~ |
|
| 280 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=7 |
|
| 281 |
+ 1.000, 2.389, 0.132, 0.192, 0.224, 0.605, 1.605, 0.183 , // H |
|
| 282 |
+ 1.000, 0.053, 3.997, 0.449, 0.201, 0.072, 0.141, 0.919 , // E |
|
| 283 |
+ 1.000, 0.109, 0.328, 2.013, 2.304, 1.882, 0.960, 1.512 , // ~ |
|
| 284 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=8 |
|
| 285 |
+ 1.000, 2.668, 0.065, 0.098, 0.144, 0.354, 1.059, 0.102 , // H |
|
| 286 |
+ 1.000, 0.029, 4.285, 0.284, 0.113, 0.044, 0.059, 0.522 , // E |
|
| 287 |
+ 1.000, 0.053, 0.200, 2.099, 2.444, 2.133, 0.671, 1.290 , // ~ |
|
| 288 |
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=9 |
|
| 289 |
+ 1.000, 2.966, 0.009, 0.023, 0.036, 0.113, 0.214, 0.017 , // H |
|
| 290 |
+ 1.000, 0.010, 4.555, 0.119, 0.027, 0.010, 0.013, 0.209 , // E |
|
| 291 |
+ 1.000, 0.026, 0.101, 2.576, 1.853, 2.204, 0.308, 0.499 // ~ |
|
| 292 |
+ }; |
|
| 293 |
+ |
|
| 294 |
+// float Ppred[]= |
|
| 295 |
+// {
|
|
| 296 |
+// //pred/obs - H E ~ S T G B |
|
| 297 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=- |
|
| 298 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 299 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 300 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 301 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=0 |
|
| 302 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 303 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 304 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 305 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=1 |
|
| 306 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 307 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 308 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 309 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=2 |
|
| 310 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 311 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 312 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 313 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=3 |
|
| 314 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 315 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 316 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 317 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=4 |
|
| 318 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 319 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 320 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 321 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=5 |
|
| 322 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 323 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 324 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 325 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=6 |
|
| 326 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 327 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 328 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 329 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=7 |
|
| 330 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 331 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 332 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 333 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=8 |
|
| 334 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 335 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 336 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 337 |
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=9 |
|
| 338 |
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H |
|
| 339 |
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E |
|
| 340 |
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~ |
|
| 341 |
+ |
|
| 342 |
+ |
|
| 343 |
+float Pobs[]={0, 0.3268,0.2119,0.2061,0.0913,0.1143,0.0376,0.0120};
|
|
| 344 |
+ |
|
| 345 |
+float Pevo_full[]= |
|
| 346 |
+ {
|
|
| 347 |
+// - H E C |
|
| 348 |
+ 1.00, 0.00, 0.00, 0.00, |
|
| 349 |
+ 0.00, 0.94, 0.00, 0.04, |
|
| 350 |
+ 0.00, 0.00, 0.92, 0.04, |
|
| 351 |
+ 0.00, 0.06, 0.08, 0.92 |
|
| 352 |
+ }; |
|
| 353 |
+ |
|
| 354 |
+//psipred accuracy for confidence values 0-9 |
|
| 355 |
+const float p_acc[]={0.00,0.47,0.53,0.56,0.58,0.62,0.69,0.74,0.82,0.88,0.96};
|
|
| 356 |
+ |
|
| 357 |
+/** |
|
| 358 |
+ * @brief |
|
| 359 |
+ */ |
|
| 360 |
+void |
|
| 361 |
+SetBlosumMatrix(const float BlosumXX[]) |
|
| 362 |
+{
|
|
| 363 |
+ int a,b,n=0; |
|
| 364 |
+ if (v>=3) printf("Using the BLOSUM%2i matrix\n",par.matrix);
|
|
| 365 |
+ for (a=0; a<20; ++a) |
|
| 366 |
+ for (pb[a]=0.0f, b=0; b<=a; ++b,++n) |
|
| 367 |
+ P[a][b] = BlosumXX[n]; |
|
| 368 |
+ for (a=0; a<19; a++) |
|
| 369 |
+ for (b=a+1; b<20; ++b) |
|
| 370 |
+ P[a][b] = P[b][a]; |
|
| 371 |
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f; |
|
| 372 |
+ return; |
|
| 373 |
+} |
|
| 374 |
+ |
|
| 375 |
+///////////////////////////////////////////////////////////////////////////////////// |
|
| 376 |
+/** |
|
| 377 |
+ * @brief Set (global variable) substitution matrix with derived matrices and background frequencies |
|
| 378 |
+ */ |
|
| 379 |
+void |
|
| 380 |
+SetSubstitutionMatrix() |
|
| 381 |
+{
|
|
| 382 |
+ int a,b; |
|
| 383 |
+ switch (par.matrix) |
|
| 384 |
+ {
|
|
| 385 |
+ default: |
|
| 386 |
+ case 0: //Gonnet matrix |
|
| 387 |
+ if (v>=3) cout<<"Using the Gonnet matrix "; |
|
| 388 |
+ for (a=0; a<20; ++a) |
|
| 389 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) |
|
| 390 |
+ P[a][b] = 0.000001f*Gonnet[a*20+b]; |
|
| 391 |
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f; |
|
| 392 |
+ break; |
|
| 393 |
+ |
|
| 394 |
+ case 30: //BLOSUM30 |
|
| 395 |
+ SetBlosumMatrix(Blosum30); |
|
| 396 |
+ break; |
|
| 397 |
+ case 40: //BLOSUM40 |
|
| 398 |
+ SetBlosumMatrix(Blosum40); |
|
| 399 |
+ break; |
|
| 400 |
+ case 50: //BLOSUM50 |
|
| 401 |
+ SetBlosumMatrix(Blosum50); |
|
| 402 |
+ break; |
|
| 403 |
+ case 65: //BLOSUM65 |
|
| 404 |
+ SetBlosumMatrix(Blosum65); |
|
| 405 |
+ break; |
|
| 406 |
+ case 80: //BLOSUM80 |
|
| 407 |
+ SetBlosumMatrix(Blosum80); |
|
| 408 |
+ break; |
|
| 409 |
+ } |
|
| 410 |
+ |
|
| 411 |
+ // Check transition probability matrix, renormalize P and calculate pb[a] |
|
| 412 |
+ float sumab=0.0f; |
|
| 413 |
+ for (a=0; a<20; a++) |
|
| 414 |
+ for (b=0; b<20; ++b) sumab+=P[a][b]; |
|
| 415 |
+ for (a=0; a<20; a++) |
|
| 416 |
+ for (b=0; b<20; ++b) P[a][b]/=sumab; |
|
| 417 |
+ for (a=0; a<20; a++) |
|
| 418 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) pb[a]+=P[a][b]; |
|
| 419 |
+ |
|
| 420 |
+ //Compute similarity matrix for amino acid pairs (for calculating consensus sequence) |
|
| 421 |
+ for (a=0; a<20; ++a) |
|
| 422 |
+ for (b=0; b<20; ++b) |
|
| 423 |
+ Sim[a][b] = P[a][b]*P[a][b]/P[a][a]/P[b][b]; |
|
| 424 |
+ |
|
| 425 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 426 |
+ for (a=0; a<20; ++a) |
|
| 427 |
+ for (b=0; b<20; ++b) |
|
| 428 |
+ R[a][b] = P[a][b]/pb[b]; //R[a][b]=P(a|b) |
|
| 429 |
+ |
|
| 430 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 431 |
+ for (a=0; a<20; ++a) |
|
| 432 |
+ for (b=0; b<20; ++b) |
|
| 433 |
+ S[a][b] = log2(R[a][b]/pb[a]); // S[a][b] = log2(P(a,b)/P(a)/P(b)) |
|
| 434 |
+ |
|
| 435 |
+ // Evaluate sequence identity underlying substitution matrix |
|
| 436 |
+ if (v>=3) |
|
| 437 |
+ {
|
|
| 438 |
+ float id=0.0f; |
|
| 439 |
+ float entropy=0.0f; |
|
| 440 |
+ float entropy_pb=0.0f; |
|
| 441 |
+ float mut_info=0.0f; |
|
| 442 |
+ for (a=0; a<20; ++a) id+=P[a][a]; |
|
| 443 |
+ for (a=0; a<20; ++a) entropy_pb-=pb[a]*log2(pb[a]); |
|
| 444 |
+ for (a=0; a<20; ++a) |
|
| 445 |
+ for (b=0; b<20; ++b) |
|
| 446 |
+ {
|
|
| 447 |
+ entropy-=P[a][b]*log2(R[a][b]); |
|
| 448 |
+ mut_info += P[a][b]*S[a][b]; |
|
| 449 |
+ } |
|
| 450 |
+ |
|
| 451 |
+ printf(": sequence identity = %2.0f%%; entropy per column = %4.2f bits (out of %4.2f); mutual information = %4.2f bits\n",100*id,entropy,entropy_pb,mut_info);
|
|
| 452 |
+ } |
|
| 453 |
+ |
|
| 454 |
+ if (v>=4) //Debugging: probability matrix and dissimilarity matrix |
|
| 455 |
+ {
|
|
| 456 |
+ cout<<"Check matrix: before renormalization sum P(a,b)= "<<sumab<<"...\n";//PRINT |
|
| 457 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 458 |
+ cout<<"p[] "; |
|
| 459 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
|
|
| 460 |
+ cout<<endl<<"\nSubstitution matrix log2( P(a,b)/p(a)/p(b) ) (in bits):\n"; |
|
| 461 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 462 |
+ for (b=0; b<20; b++) |
|
| 463 |
+ {
|
|
| 464 |
+ cout<<i2aa(b)<<" "; |
|
| 465 |
+ for (a=0; a<20; a++) printf("%4.1f ",S[a][b]);
|
|
| 466 |
+ cout<<endl; |
|
| 467 |
+ } |
|
| 468 |
+ cout<<endl<<"\nOdds matrix P(a,b)/p(a)/p(b):\n"; |
|
| 469 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 470 |
+ for (b=0; b<20; b++) |
|
| 471 |
+ {
|
|
| 472 |
+ cout<<i2aa(b)<<" "; |
|
| 473 |
+ for (a=0; a<20; a++) printf("%4.1f ",P[b][a]/pb[a]/pb[b]);
|
|
| 474 |
+ cout<<endl; |
|
| 475 |
+ } |
|
| 476 |
+ cout<<endl<<"\nMatrix of conditional probabilities P(a|b) = P(a,b)/p(b) (in %):\n"; |
|
| 477 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 478 |
+ for (b=0; b<20; b++) |
|
| 479 |
+ {
|
|
| 480 |
+ cout<<i2aa(b)<<" "; |
|
| 481 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*R[b][a]);
|
|
| 482 |
+ cout<<endl; |
|
| 483 |
+ } |
|
| 484 |
+ cout<<endl<<"\nProbability matrix P(a,b) (in %):\n"; |
|
| 485 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 486 |
+ for (b=0; b<20; b++) |
|
| 487 |
+ {
|
|
| 488 |
+ cout<<i2aa(b)<<" "; |
|
| 489 |
+ for (a=0; a<20; a++) printf("%5.0f ",1000000*P[b][a]);
|
|
| 490 |
+ cout<<endl; |
|
| 491 |
+ } |
|
| 492 |
+ cout<<endl<<"Similarity matrix P(a,b)^2/P(a,a,)/P(b,b) (in %):\n"; |
|
| 493 |
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n"; |
|
| 494 |
+ for (b=0; b<20; b++) |
|
| 495 |
+ {
|
|
| 496 |
+ cout<<i2aa(b)<<" "; |
|
| 497 |
+ for (a=0; a<20; a++) printf("%4.0f ",100*Sim[b][a]);
|
|
| 498 |
+ cout<<endl; |
|
| 499 |
+ } |
|
| 500 |
+ cout<<endl; |
|
| 501 |
+ |
|
| 502 |
+ |
|
| 503 |
+ } |
|
| 504 |
+} |
|
| 505 |
+ |
|
| 506 |
+///////////////////////////////////////////////////////////////////////////////////// |
|
| 507 |
+/** |
|
| 508 |
+ * @brief Set (global variable) substitution matrix with derived matrices and background frequencies |
|
| 509 |
+ */ |
|
| 510 |
+void |
|
| 511 |
+SetRnaSubstitutionMatrix() |
|
| 512 |
+{
|
|
| 513 |
+ printf("SET RNA SUBSTITUTION MATRIX ....");
|
|
| 514 |
+ int a,b; |
|
| 515 |
+ for (a=0; a<20; ++a) |
|
| 516 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) |
|
| 517 |
+ P[a][b] = 0.000001f*ribosum[a*20+b]; |
|
| 518 |
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f; |
|
| 519 |
+ |
|
| 520 |
+ // Check transition probability matrix, renormalize P and calculate pb[a] |
|
| 521 |
+ float sumab=0.0f; |
|
| 522 |
+ for (a=0; a<20; a++) |
|
| 523 |
+ for (b=0; b<20; ++b) sumab+=P[a][b]; |
|
| 524 |
+ for (a=0; a<20; a++) |
|
| 525 |
+ for (b=0; b<20; ++b) P[a][b]/=sumab; |
|
| 526 |
+ for (a=0; a<20; a++) |
|
| 527 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) pb[a]+=P[a][b]; |
|
| 528 |
+ |
|
| 529 |
+ //Compute similarity matrix for amino acid pairs (for calculating consensus sequence) |
|
| 530 |
+ for (a=0; a<20; ++a) |
|
| 531 |
+ for (b=0; b<20; ++b) |
|
| 532 |
+ Sim[a][b] = P[a][b]*P[a][b]/P[a][a]/P[b][b]; |
|
| 533 |
+ |
|
| 534 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 535 |
+ for (a=0; a<20; ++a) |
|
| 536 |
+ for (b=0; b<20; ++b) |
|
| 537 |
+ R[a][b] = P[a][b]/pb[b]; //R[a][b]=P(a|b) |
|
| 538 |
+ |
|
| 539 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 540 |
+ for (a=0; a<20; ++a) |
|
| 541 |
+ for (b=0; b<20; ++b) |
|
| 542 |
+ S[a][b] = log2(R[a][b]/pb[a]); // S[a][b] = log2(P(a,b)/P(a)/P(b)) |
|
| 543 |
+ |
|
| 544 |
+ // Evaluate sequence identity underlying substitution matrix |
|
| 545 |
+ if (v>=3) |
|
| 546 |
+ {
|
|
| 547 |
+ float id=0.0f; |
|
| 548 |
+ float entropy=0.0f; |
|
| 549 |
+ float entropy_pb=0.0f; |
|
| 550 |
+ float mut_info=0.0f; |
|
| 551 |
+ for (a=0; a<20; ++a) id+=P[a][a]; |
|
| 552 |
+ for (a=0; a<20; ++a) entropy_pb-=pb[a]*log2(pb[a]); |
|
| 553 |
+ for (a=0; a<20; ++a) |
|
| 554 |
+ for (b=0; b<20; ++b) |
|
| 555 |
+ {
|
|
| 556 |
+ entropy-=P[a][b]*log2(R[a][b]); |
|
| 557 |
+ mut_info += P[a][b]*S[a][b]; |
|
| 558 |
+ } |
|
| 559 |
+ |
|
| 560 |
+ printf(": sequence identity = %2.0f%%; entropy per column = %4.2f bits (out of %4.2f); mutual information = %4.2f bits\n",100*id,entropy,entropy_pb,mut_info);
|
|
| 561 |
+ } |
|
| 562 |
+ |
|
| 563 |
+ if (v>=4) //Debugging: probability matrix and dissimilarity matrix |
|
| 564 |
+ {
|
|
| 565 |
+ cout<<"Check matrix: before renormalization sum P(a,b)= "<<sumab<<"...\n";//PRINT |
|
| 566 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 567 |
+ cout<<"p[] "; |
|
| 568 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
|
|
| 569 |
+ cout<<endl<<"\nSubstitution matrix log2( P(a,b)/p(a)/p(b) ) (in bits):\n"; |
|
| 570 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 571 |
+ for (b=0; b<20; b++) |
|
| 572 |
+ {
|
|
| 573 |
+ cout<<i2aa(b)<<" "; |
|
| 574 |
+ for (a=0; a<20; a++) printf("%4.1f ",S[a][b]);
|
|
| 575 |
+ cout<<endl; |
|
| 576 |
+ } |
|
| 577 |
+ cout<<endl<<"\nOdds matrix P(a,b)/p(a)/p(b):\n"; |
|
| 578 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 579 |
+ for (b=0; b<20; b++) |
|
| 580 |
+ {
|
|
| 581 |
+ cout<<i2aa(b)<<" "; |
|
| 582 |
+ for (a=0; a<20; a++) printf("%4.1f ",P[b][a]/pb[a]/pb[b]);
|
|
| 583 |
+ cout<<endl; |
|
| 584 |
+ } |
|
| 585 |
+ cout<<endl<<"\nMatrix of conditional probabilities P(a|b) = P(a,b)/p(b) (in %):\n"; |
|
| 586 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 587 |
+ for (b=0; b<20; b++) |
|
| 588 |
+ {
|
|
| 589 |
+ cout<<i2aa(b)<<" "; |
|
| 590 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*R[b][a]);
|
|
| 591 |
+ cout<<endl; |
|
| 592 |
+ } |
|
| 593 |
+ cout<<endl<<"\nProbability matrix P(a,b) (in %):\n"; |
|
| 594 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 595 |
+ for (b=0; b<20; b++) |
|
| 596 |
+ {
|
|
| 597 |
+ cout<<i2aa(b)<<" "; |
|
| 598 |
+ for (a=0; a<20; a++) printf("%5.0f ",1000000*P[b][a]);
|
|
| 599 |
+ cout<<endl; |
|
| 600 |
+ } |
|
| 601 |
+ cout<<endl<<"Similarity matrix P(a,b)^2/P(a,a,)/P(b,b) (in %):\n"; |
|
| 602 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 603 |
+ for (b=0; b<20; b++) |
|
| 604 |
+ {
|
|
| 605 |
+ cout<<i2aa(b)<<" "; |
|
| 606 |
+ for (a=0; a<20; a++) printf("%4.0f ",100*Sim[b][a]);
|
|
| 607 |
+ cout<<endl; |
|
| 608 |
+ } |
|
| 609 |
+ cout<<endl; |
|
| 610 |
+ |
|
| 611 |
+ |
|
| 612 |
+ } |
|
| 613 |
+} |
|
| 614 |
+ |
|
| 615 |
+///////////////////////////////////////////////////////////////////////////////////// |
|
| 616 |
+/** |
|
| 617 |
+ * @brief Set (global variable) substitution matrix with derived matrices and background frequencies |
|
| 618 |
+ */ |
|
| 619 |
+void |
|
| 620 |
+SetDnaSubstitutionMatrix() |
|
| 621 |
+{
|
|
| 622 |
+ |
|
| 623 |
+ int a,b; |
|
| 624 |
+ for (a=0; a<20; ++a) |
|
| 625 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) |
|
| 626 |
+ P[a][b] = 0.000001f*dna_basic[a*20+b]; |
|
| 627 |
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f; |
|
| 628 |
+ |
|
| 629 |
+ // Check transition probability matrix, renormalize P and calculate pb[a] |
|
| 630 |
+ float sumab=0.0f; |
|
| 631 |
+ for (a=0; a<20; a++) |
|
| 632 |
+ for (b=0; b<20; ++b) sumab+=P[a][b]; |
|
| 633 |
+ for (a=0; a<20; a++) |
|
| 634 |
+ for (b=0; b<20; ++b) P[a][b]/=sumab; |
|
| 635 |
+ for (a=0; a<20; a++) |
|
| 636 |
+ for (pb[a]=0.0f, b=0; b<20; ++b) pb[a]+=P[a][b]; |
|
| 637 |
+ |
|
| 638 |
+ //Compute similarity matrix for amino acid pairs (for calculating consensus sequence) |
|
| 639 |
+ for (a=0; a<20; ++a) |
|
| 640 |
+ for (b=0; b<20; ++b) |
|
| 641 |
+ Sim[a][b] = P[a][b]*P[a][b]/P[a][a]/P[b][b]; |
|
| 642 |
+ |
|
| 643 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 644 |
+ for (a=0; a<20; ++a) |
|
| 645 |
+ for (b=0; b<20; ++b) |
|
| 646 |
+ R[a][b] = P[a][b]/pb[b]; //R[a][b]=P(a|b) |
|
| 647 |
+ |
|
| 648 |
+ //Precompute matrix R for amino acid pseudocounts: |
|
| 649 |
+ for (a=0; a<20; ++a) |
|
| 650 |
+ for (b=0; b<20; ++b) |
|
| 651 |
+ S[a][b] = log2(R[a][b]/pb[a]); // S[a][b] = log2(P(a,b)/P(a)/P(b)) |
|
| 652 |
+ |
|
| 653 |
+ // Evaluate sequence identity underlying substitution matrix |
|
| 654 |
+ if (v>=3) |
|
| 655 |
+ {
|
|
| 656 |
+ float id=0.0f; |
|
| 657 |
+ float entropy=0.0f; |
|
| 658 |
+ float entropy_pb=0.0f; |
|
| 659 |
+ float mut_info=0.0f; |
|
| 660 |
+ for (a=0; a<20; ++a) id+=P[a][a]; |
|
| 661 |
+ for (a=0; a<20; ++a) entropy_pb-=pb[a]*log2(pb[a]); |
|
| 662 |
+ for (a=0; a<20; ++a) |
|
| 663 |
+ for (b=0; b<20; ++b) |
|
| 664 |
+ {
|
|
| 665 |
+ entropy-=P[a][b]*log2(R[a][b]); |
|
| 666 |
+ mut_info += P[a][b]*S[a][b]; |
|
| 667 |
+ } |
|
| 668 |
+ |
|
| 669 |
+ printf(": sequence identity = %2.0f%%; entropy per column = %4.2f bits (out of %4.2f); mutual information = %4.2f bits\n",100*id,entropy,entropy_pb,mut_info);
|
|
| 670 |
+ } |
|
| 671 |
+ |
|
| 672 |
+ if (v>=4) //Debugging: probability matrix and dissimilarity matrix |
|
| 673 |
+ {
|
|
| 674 |
+ cout<<"Check matrix: before renormalization sum P(a,b)= "<<sumab<<"...\n";//PRINT |
|
| 675 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 676 |
+ cout<<"p[] "; |
|
| 677 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
|
|
| 678 |
+ cout<<endl<<"\nSubstitution matrix log2( P(a,b)/p(a)/p(b) ) (in bits):\n"; |
|
| 679 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 680 |
+ for (b=0; b<20; b++) |
|
| 681 |
+ {
|
|
| 682 |
+ cout<<i2aa(b)<<" "; |
|
| 683 |
+ for (a=0; a<20; a++) printf("%4.1f ",S[a][b]);
|
|
| 684 |
+ cout<<endl; |
|
| 685 |
+ } |
|
| 686 |
+ cout<<endl<<"\nOdds matrix P(a,b)/p(a)/p(b):\n"; |
|
| 687 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 688 |
+ for (b=0; b<20; b++) |
|
| 689 |
+ {
|
|
| 690 |
+ cout<<i2aa(b)<<" "; |
|
| 691 |
+ for (a=0; a<20; a++) printf("%4.1f ",P[b][a]/pb[a]/pb[b]);
|
|
| 692 |
+ cout<<endl; |
|
| 693 |
+ } |
|
| 694 |
+ cout<<endl<<"\nMatrix of conditional probabilities P(a|b) = P(a,b)/p(b) (in %):\n"; |
|
| 695 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 696 |
+ for (b=0; b<20; b++) |
|
| 697 |
+ {
|
|
| 698 |
+ cout<<i2aa(b)<<" "; |
|
| 699 |
+ for (a=0; a<20; a++) printf("%4.1f ",100*R[b][a]);
|
|
| 700 |
+ cout<<endl; |
|
| 701 |
+ } |
|
| 702 |
+ cout<<endl<<"\nProbability matrix P(a,b) (in %):\n"; |
|
| 703 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 704 |
+ for (b=0; b<20; b++) |
|
| 705 |
+ {
|
|
| 706 |
+ cout<<i2aa(b)<<" "; |
|
| 707 |
+ for (a=0; a<20; a++) printf("%5.0f ",1000000*P[b][a]);
|
|
| 708 |
+ cout<<endl; |
|
| 709 |
+ } |
|
| 710 |
+ cout<<endl<<"Similarity matrix P(a,b)^2/P(a,a,)/P(b,b) (in %):\n"; |
|
| 711 |
+ cout<<" A C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\n"; |
|
| 712 |
+ for (b=0; b<20; b++) |
|
| 713 |
+ {
|
|
| 714 |
+ cout<<i2aa(b)<<" "; |
|
| 715 |
+ for (a=0; a<20; a++) printf("%4.0f ",100*Sim[b][a]);
|
|
| 716 |
+ cout<<endl; |
|
| 717 |
+ } |
|
| 718 |
+ cout<<endl; |
|
| 719 |
+ |
|
| 720 |
+ |
|
| 721 |
+ } |
|
| 722 |
+} |
|
| 723 |
+ |
|
| 724 |
+///////////////////////////////////////////////////////////////////////////////////// |
|
| 725 |
+/** |
|
| 726 |
+ * @brief Set secondary structure substitution matrix |
|
| 727 |
+ */ |
|
| 728 |
+void |
|
| 729 |
+SetSecStrucSubstitutionMatrix() |
|
| 730 |
+{
|
|
| 731 |
+ int A; //observed ss state (determined dssp) |
|
| 732 |
+ int B,BB; //predicted ss states (by psipred) |
|
| 733 |
+ int cf,ccf; //confidence value of prediction |
|
| 734 |
+ float P73[NDSSP][NSSPRED][MAXCF]; //P73[cf][B][A] = P(A,B,cf)/P(A)/P(B,cf) = P(A|B,cf)/P(A) |
|
| 735 |
+ float sum; |
|
| 736 |
+ |
|
| 737 |
+ // S73[A][B][cf][b] = score for matching observed ss state A in query with state B in template |
|
| 738 |
+ // predicted with confidence cf, when query and template columns are diverged by b units |
|
| 739 |
+ for (cf=0; cf<MAXCF; cf++) |
|
| 740 |
+ for (A=0; A<NDSSP; A++) |
|
| 741 |
+ for (B=0; B<NSSPRED; B++) |
|
| 742 |
+ {
|
|
| 743 |
+ P73[A][B][cf] = 1.-par.ssa + par.ssa*Ppred[cf*NSSPRED*NDSSP + B*NDSSP + A]; |
|
| 744 |
+ S73[A][B][cf] = log2(P73[A][B][cf]); |
|
| 745 |
+ } |
|
| 746 |
+ |
|
| 747 |
+ for (B=0; B<NSSPRED; B++) |
|
| 748 |
+ for (cf=0; cf<MAXCF; cf++) |
|
| 749 |
+ for (BB=0; BB<NSSPRED; BB++) |
|
| 750 |
+ for (ccf=0; ccf<MAXCF; ccf++) |
|
| 751 |
+ {
|
|
| 752 |
+ sum=0; |
|
| 753 |
+ for (A=1; A<NDSSP; A++) |
|
| 754 |
+ sum += P73[A][B][cf] * P73[A][BB][ccf] * Pobs[A]; |
|
| 755 |
+ S33[B][cf][BB][ccf] = log2(sum); |
|
| 756 |
+ } |
|
| 757 |
+} /* this is the end of SetSecStrucSubstitutionMatrix() */ |
|
| 758 |
+ |
|
| 759 |
+ |
|
| 760 |
+ |
|
| 761 |
+/* |
|
| 762 |
+ * EOF hhmatrices-C.h |
|
| 763 |
+ */ |