| 1 | /* DAYHOFF.H |
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| 2 | |
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| 3 | Table of estimated PAMS (actual no. of substitutions per 100 residues) |
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| 4 | for a range of observed amino acid distances from 75.0% (the first entry |
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| 5 | in the array), in 0.1% increments, up to 93.0%. |
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| 6 | |
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| 7 | These values are used to correct for multiple hits in protein alignments. |
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| 8 | The values below are for observed distances above 74.9%. For values above |
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| 9 | 93%, an arbitrary value of 1000 PAMS (1000% substitution) is used. |
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| 10 | |
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| 11 | These values are derived from a Dayhoff model (1978) of amino acid |
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| 12 | substitution and assume average amino acid composition and that amino |
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| 13 | acids replace each other at the same rate as in the original Dayhoff model. |
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| 14 | |
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| 15 | Up to 75% observed distance, use Kimura's emprical formula to derive |
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| 16 | the correction. For 75% or greater, use this table. Kimura's formula |
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| 17 | is accurate up to about 75% and fails completely above 85%. |
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| 18 | */ |
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| 19 | |
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| 20 | int dayhoff_pams[]={ |
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| 21 | 195, /* 75.0% observed d; 195 PAMs estimated = 195% estimated d */ |
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| 22 | 196, /* 75.1% observed d; 196 PAMs estimated */ |
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| 23 | 197, 198, 199, 200, 200, 201, 202, 203, |
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| 24 | 204, 205, 206, 207, 208, 209, 209, 210, 211, 212, |
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| 25 | 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, |
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| 26 | 223, 224, 226, 227, 228, 229, 230, 231, 232, 233, |
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| 27 | 234, 236, 237, 238, 239, 240, 241, 243, 244, 245, |
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| 28 | 246, 248, 249, 250, /* 250 PAMs = 80.3% observed d */ |
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| 29 | 252, 253, 254, 255, 257, 258, |
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| 30 | 260, 261, 262, 264, 265, 267, 268, 270, 271, 273, |
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| 31 | 274, 276, 277, 279, 281, 282, 284, 285, 287, 289, |
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| 32 | 291, 292, 294, 296, 298, 299, 301, 303, 305, 307, |
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| 33 | 309, 311, 313, 315, 317, 319, 321, 323, 325, 328, |
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| 34 | 330, 332, 335, 337, 339, 342, 344, 347, 349, 352, |
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| 35 | 354, 357, 360, 362, 365, 368, 371, 374, 377, 380, |
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| 36 | 383, 386, 389, 393, 396, 399, 403, 407, 410, 414, |
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| 37 | 418, 422, 426, 430, 434, 438, 442, 447, 451, 456, |
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| 38 | 461, 466, 471, 476, 482, 487, 493, 498, 504, 511, |
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| 39 | 517, 524, 531, 538, 545, 553, 560, 569, 577, 586, |
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| 40 | 595, 605, 615, 626, 637, 649, 661, 675, 688, 703, |
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| 41 | 719, 736, 754, 775, 796, 819, 845, 874, 907, 945, |
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| 42 | /* 92.9% observed; 945 PAMs */ |
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| 43 | 988 /* 93.0% observed; 988 PAMs */ |
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| 44 | }; |
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| 45 | |
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