# This file is the result of combining several RDB files, specifically # T0578.t04.dssp-ebghstl.rdb (weight 1.53986) # T0578.t04.stride-ebghtl.rdb (weight 1.24869) # T0578.t04.str2.rdb (weight 1.54758) # T0578.t04.alpha.rdb (weight 0.659012) # T0578.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0578.t2k.stride-ebghtl.rdb (weight 1.24869) # T0578.t2k.str2.rdb (weight 1.54758) # T0578.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 T0578.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0578 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0578.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 7.82799 # # ============================================ # Comments from T0578.t04.stride-ebghtl.rdb # ============================================ # TARGET T0578 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0578.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 7.82799 # # ============================================ # Comments from T0578.t04.str2.rdb # ============================================ # TARGET T0578 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0578.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 7.82799 # # ============================================ # Comments from T0578.t04.alpha.rdb # ============================================ # TARGET T0578 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0578.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 7.82799 # # ============================================ # Comments from T0578.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ # Comments from T0578.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ # Comments from T0578.t2k.str2.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ # Comments from T0578.t2k.alpha.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0401 0.2901 0.6698 2 N 0.0627 0.6156 0.3217 3 A 0.0424 0.7331 0.2245 4 M 0.0595 0.7503 0.1902 5 K 0.0410 0.7556 0.2034 6 K 0.0449 0.7103 0.2449 7 A 0.0226 0.6571 0.3203 8 T 0.0278 0.3655 0.6067 9 M 0.0113 0.7101 0.2786 10 L 0.0059 0.9091 0.0850 11 T 0.0051 0.9297 0.0651 12 Y 0.0049 0.9450 0.0501 13 L 0.0053 0.9444 0.0503 14 E 0.0049 0.9425 0.0526 15 E 0.0058 0.9411 0.0531 16 Q 0.0058 0.9308 0.0634 17 L 0.0112 0.8931 0.0957 18 E 0.0107 0.8278 0.1615 19 K 0.0189 0.6638 0.3173 20 H 0.0432 0.3209 0.6359 21 L 0.0623 0.1480 0.7897 22 G 0.1137 0.0622 0.8242 23 D 0.1112 0.0750 0.8138 24 Y 0.2607 0.0669 0.6723 25 E 0.4520 0.0594 0.4885 26 V 0.6910 0.0546 0.2544 27 G 0.7488 0.0398 0.2114 28 L 0.6739 0.0438 0.2823 29 D 0.5257 0.0358 0.4385 30 W 0.2742 0.1136 0.6122 31 D 0.2268 0.0760 0.6972 32 R 0.0981 0.1484 0.7536 33 K 0.0660 0.1495 0.7844 34 N 0.1447 0.0663 0.7890 35 H 0.3242 0.0283 0.6475 36 T 0.7599 0.0069 0.2333 37 I 0.9006 0.0036 0.0959 38 E 0.9195 0.0033 0.0771 39 V 0.9187 0.0032 0.0780 40 I 0.9266 0.0032 0.0703 41 V 0.9271 0.0033 0.0696 42 R 0.9282 0.0032 0.0686 43 L 0.9218 0.0040 0.0743 44 Y 0.9086 0.0053 0.0862 45 A 0.8635 0.0091 0.1274 46 E 0.5782 0.0437 0.3781 47 N 0.3342 0.0230 0.6428 48 N 0.0388 0.2657 0.6955 49 E 0.0543 0.2162 0.7295 50 Q 0.2077 0.2621 0.5302 51 V 0.5478 0.0201 0.4321 52 A 0.8433 0.0053 0.1514 53 I 0.8505 0.0069 0.1426 54 D 0.8184 0.0117 0.1698 55 D 0.4317 0.0158 0.5525 56 V 0.1293 0.1242 0.7466 57 D 0.1278 0.0290 0.8432 58 G 0.1727 0.0392 0.7881 59 T 0.4200 0.0205 0.5596 60 L 0.6278 0.0158 0.3564 61 S 0.2186 0.0228 0.7587 62 E 0.0683 0.1478 0.7839 63 E 0.0639 0.1192 0.8169 64 E 0.1096 0.1443 0.7461 65 F 0.4367 0.0823 0.4809 66 I 0.6647 0.0388 0.2964 67 E 0.7594 0.0192 0.2214 68 F 0.7295 0.0347 0.2358 69 E 0.6106 0.0589 0.3306 70 D 0.6419 0.0434 0.3148 71 G 0.8201 0.0192 0.1607 72 L 0.8803 0.0085 0.1112 73 L 0.8897 0.0101 0.1002 74 F 0.8243 0.0177 0.1579 75 Y 0.5766 0.0219 0.4015 76 N 0.2426 0.0163 0.7410 77 P 0.0188 0.2785 0.7027 78 Q 0.0195 0.3367 0.6438 79 K 0.0473 0.4145 0.5382 80 S 0.0972 0.1793 0.7236 81 V 0.2065 0.1301 0.6634 82 V 0.2960 0.0615 0.6425 83 D 0.1575 0.0464 0.7961 84 D 0.0300 0.6246 0.3454 85 E 0.0235 0.5354 0.4411 86 E 0.0549 0.4694 0.4756 87 Y 0.3379 0.1525 0.5096 88 L 0.6519 0.0528 0.2952 89 V 0.8138 0.0296 0.1566 90 T 0.8163 0.0293 0.1544 91 I 0.7293 0.0143 0.2563 92 P 0.5040 0.0191 0.4769 93 Y 0.1618 0.0647 0.7735 94 E 0.1063 0.1129 0.7809 95 G 0.0393 0.1974 0.7632 96 K 0.0457 0.2757 0.6786 97 K 0.0605 0.1890 0.7505 98 G 0.0566 0.1244 0.8190 99 L 0.1008 0.1865 0.7127 100 R 0.1140 0.3246 0.5613 101 K 0.0048 0.9392 0.0560 102 A 0.0047 0.9505 0.0448 103 V 0.0047 0.9548 0.0405 104 L 0.0047 0.9597 0.0356 105 D 0.0047 0.9602 0.0351 106 G 0.0047 0.9601 0.0353 107 F 0.0047 0.9598 0.0356 108 I 0.0047 0.9599 0.0355 109 H 0.0047 0.9590 0.0363 110 Y 0.0047 0.9582 0.0371 111 L 0.0047 0.9579 0.0374 112 K 0.0047 0.9588 0.0365 113 V 0.0047 0.9576 0.0377 114 V 0.0050 0.9531 0.0419 115 L 0.0060 0.9404 0.0536 116 D 0.0063 0.8914 0.1023 117 E 0.0337 0.5959 0.3704 118 G 0.0427 0.2944 0.6629 119 Q 0.0248 0.5575 0.4177 120 S 0.0259 0.7103 0.2638 121 D 0.0170 0.7665 0.2165 122 L 0.0156 0.8448 0.1397 123 L 0.0146 0.8444 0.1410 124 D 0.0150 0.7933 0.1917 125 F 0.0311 0.6325 0.3364 126 L 0.0826 0.3767 0.5407 127 S 0.0707 0.1489 0.7804 128 D 0.0738 0.0496 0.8766 129 E 0.0257 0.2268 0.7475 130 T 0.0462 0.2329 0.7210 131 A 0.0824 0.2558 0.6618 132 E 0.2094 0.1283 0.6624 133 V 0.6338 0.0441 0.3221 134 F 0.7835 0.0200 0.1966 135 E 0.8695 0.0097 0.1208 136 L 0.8335 0.0174 0.1491 137 H 0.7600 0.0110 0.2291 138 W 0.4050 0.0276 0.5674 139 E 0.1286 0.0153 0.8560 140 P 0.0060 0.8607 0.1333 141 A 0.0050 0.9221 0.0729 142 D 0.0051 0.9297 0.0652 143 F 0.0048 0.9427 0.0524 144 E 0.0055 0.9379 0.0566 145 A 0.0060 0.9223 0.0717 146 M 0.0060 0.9076 0.0864 147 I 0.0091 0.9019 0.0890 148 K 0.0091 0.8510 0.1399 149 K 0.0139 0.7655 0.2206 150 V 0.0225 0.6927 0.2847 151 A 0.0210 0.7376 0.2414 152 E 0.0176 0.7196 0.2628 153 T 0.0298 0.5783 0.3919 154 E 0.0513 0.4581 0.4906 155 K 0.0611 0.2721 0.6668 156 E 0.1108 0.1736 0.7156 157 Q 0.1249 0.1574 0.7177 158 W 0.1250 0.1174 0.7576 159 I 0.0800 0.0600 0.8600 160 A 0.0835 0.0836 0.8329 161 Y 0.1126 0.0726 0.8148 162 P 0.1156 0.0671 0.8173 163 S 0.1251 0.0724 0.8024 164 Y 0.0604 0.0272 0.9124