# This file is the result of combining several RDB files, specifically # T0385.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0385.t2k.stride-ebghtl.rdb (weight 1.24869) # T0385.t2k.str2.rdb (weight 1.54758) # T0385.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0385.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0385 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0385.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0385.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0385 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0385.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0385.t2k.str2.rdb # ============================================ # TARGET T0385 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0385.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0385.t2k.alpha.rdb # ============================================ # TARGET T0385 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0385.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0739 0.0409 0.8853 2 T 0.1538 0.0697 0.7766 3 S 0.1323 0.1174 0.7503 4 S 0.1138 0.1174 0.7687 5 E 0.1032 0.0860 0.8108 6 P 0.0969 0.1004 0.8027 7 A 0.0835 0.1500 0.7665 8 H 0.0742 0.2026 0.7232 9 G 0.0996 0.2061 0.6943 10 A 0.1201 0.1690 0.7108 11 T 0.1246 0.1139 0.7616 12 P 0.0904 0.1265 0.7831 13 K 0.0862 0.1106 0.8032 14 R 0.0921 0.0955 0.8124 15 S 0.0824 0.0874 0.8303 16 P 0.0424 0.2400 0.7176 17 S 0.0506 0.1902 0.7592 18 E 0.0439 0.2204 0.7357 19 G 0.0396 0.4010 0.5594 20 S 0.0153 0.7607 0.2240 21 A 0.0108 0.8320 0.1572 22 D 0.0086 0.8742 0.1172 23 N 0.0056 0.9259 0.0686 24 A 0.0057 0.9348 0.0596 25 A 0.0054 0.9429 0.0517 26 L 0.0048 0.9504 0.0448 27 C 0.0048 0.9547 0.0405 28 D 0.0048 0.9544 0.0408 29 A 0.0049 0.9520 0.0431 30 L 0.0050 0.9459 0.0491 31 A 0.0049 0.9399 0.0551 32 V 0.0049 0.9370 0.0582 33 E 0.0048 0.9462 0.0490 34 H 0.0051 0.9536 0.0414 35 A 0.0050 0.9544 0.0406 36 T 0.0051 0.9517 0.0432 37 I 0.0055 0.9532 0.0413 38 Y 0.0057 0.9488 0.0456 39 G 0.0073 0.9367 0.0560 40 Y 0.0112 0.9167 0.0721 41 G 0.0218 0.8893 0.0889 42 I 0.0395 0.8803 0.0802 43 V 0.0491 0.8508 0.1001 44 S 0.0753 0.7714 0.1533 45 A 0.1219 0.5911 0.2870 46 L 0.1553 0.3525 0.4922 47 S 0.1290 0.0951 0.7758 48 P 0.0642 0.0515 0.8843 49 P 0.0107 0.6746 0.3147 50 G 0.0108 0.6934 0.2958 51 V 0.0120 0.8052 0.1828 52 N 0.0084 0.8622 0.1294 53 F 0.0063 0.9136 0.0801 54 L 0.0056 0.9397 0.0547 55 V 0.0055 0.9516 0.0429 56 A 0.0049 0.9575 0.0375 57 D 0.0047 0.9560 0.0393 58 A 0.0048 0.9508 0.0444 59 L 0.0047 0.9523 0.0429 60 K 0.0049 0.9401 0.0550 61 Q 0.0056 0.9149 0.0795 62 H 0.0086 0.9002 0.0911 63 R 0.0057 0.9209 0.0735 64 H 0.0060 0.9230 0.0710 65 R 0.0065 0.9197 0.0737 66 R 0.0055 0.9473 0.0472 67 D 0.0052 0.9524 0.0424 68 D 0.0048 0.9551 0.0401 69 V 0.0047 0.9566 0.0387 70 I 0.0047 0.9572 0.0380 71 V 0.0048 0.9540 0.0412 72 M 0.0049 0.9442 0.0510 73 L 0.0063 0.9288 0.0649 74 S 0.0077 0.8858 0.1065 75 A 0.0101 0.7987 0.1912 76 R 0.0436 0.4941 0.4623 77 G 0.0531 0.1429 0.8040 78 V 0.0740 0.0707 0.8553 79 T 0.0907 0.0511 0.8583 80 A 0.0822 0.0619 0.8559 81 P 0.0989 0.0784 0.8227 82 I 0.1059 0.1364 0.7577 83 A 0.0811 0.2294 0.6895 84 A 0.0617 0.3620 0.5763 85 A 0.0366 0.4498 0.5136 86 G 0.0544 0.3609 0.5847 87 Y 0.1339 0.2317 0.6344 88 Q 0.1879 0.1118 0.7003 89 L 0.1753 0.0365 0.7882 90 P 0.1700 0.0225 0.8075 91 M 0.2138 0.0266 0.7596 92 Q 0.1634 0.0228 0.8139 93 V 0.1133 0.0334 0.8532 94 S 0.0610 0.0481 0.8909 95 S 0.0656 0.0221 0.9123 96 A 0.0060 0.8551 0.1389 97 A 0.0053 0.8945 0.1002 98 D 0.0058 0.9223 0.0719 99 A 0.0048 0.9477 0.0476 100 A 0.0047 0.9535 0.0418 101 R 0.0047 0.9484 0.0468 102 L 0.0048 0.9472 0.0480 103 A 0.0048 0.9477 0.0475 104 V 0.0048 0.9382 0.0570 105 R 0.0050 0.9124 0.0826 106 M 0.0055 0.9148 0.0797 107 E 0.0054 0.9244 0.0702 108 N 0.0060 0.9130 0.0811 109 D 0.0071 0.8628 0.1300 110 G 0.0050 0.9153 0.0798 111 A 0.0047 0.9422 0.0530 112 T 0.0047 0.9538 0.0415 113 A 0.0047 0.9565 0.0387 114 W 0.0047 0.9584 0.0369 115 R 0.0047 0.9577 0.0376 116 A 0.0048 0.9535 0.0417 117 V 0.0049 0.9450 0.0501 118 V 0.0058 0.9238 0.0704 119 E 0.0066 0.8138 0.1796 120 H 0.0134 0.6603 0.3262 121 A 0.0505 0.4124 0.5371 122 E 0.0498 0.1916 0.7586 123 T 0.0523 0.0735 0.8742 124 A 0.0061 0.8543 0.1395 125 D 0.0054 0.8993 0.0952 126 D 0.0050 0.9402 0.0548 127 R 0.0047 0.9540 0.0412 128 V 0.0047 0.9563 0.0390 129 F 0.0047 0.9558 0.0395 130 A 0.0047 0.9554 0.0399 131 S 0.0047 0.9576 0.0377 132 T 0.0048 0.9548 0.0405 133 A 0.0048 0.9479 0.0473 134 L 0.0049 0.9399 0.0552 135 T 0.0053 0.9366 0.0581 136 E 0.0054 0.9394 0.0552 137 S 0.0051 0.9487 0.0462 138 A 0.0049 0.9472 0.0479 139 V 0.0048 0.9518 0.0433 140 M 0.0048 0.9522 0.0430 141 A 0.0049 0.9492 0.0459 142 T 0.0058 0.9421 0.0521 143 R 0.0072 0.9227 0.0701 144 W 0.0100 0.8779 0.1121 145 N 0.0166 0.7875 0.1958 146 R 0.0244 0.6775 0.2981 147 V 0.0444 0.5363 0.4193 148 L 0.0610 0.3076 0.6314 149 G 0.0590 0.1195 0.8214 150 A 0.0988 0.0907 0.8105 151 W 0.1636 0.0451 0.7913 152 P 0.2262 0.0649 0.7090 153 I 0.4047 0.0714 0.5239 154 T 0.4816 0.0879 0.4305 155 A 0.4254 0.1071 0.4675 156 A 0.2907 0.1069 0.6025 157 F 0.1755 0.0540 0.7705 158 P 0.0898 0.1209 0.7893 159 G 0.0815 0.0936 0.8248 160 G 0.0909 0.0832 0.8260 161 D 0.0799 0.0720 0.8481 162 E 0.0337 0.0620 0.9043