# This file is the result of combining several RDB files, specifically # T0590.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0590.t2k.stride-ebghtl.rdb (weight 1.24869) # T0590.t2k.str2.rdb (weight 1.54758) # T0590.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 T0590.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0590 # 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 T0590.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 1316 # # ============================================ # Comments from T0590.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0590 # 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 T0590.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 1316 # # ============================================ # Comments from T0590.t2k.str2.rdb # ============================================ # TARGET T0590 # 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 T0590.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 1316 # # ============================================ # Comments from T0590.t2k.alpha.rdb # ============================================ # TARGET T0590 # 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 T0590.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 1316 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0885 0.0365 0.8750 2 N 0.0878 0.0406 0.8716 3 A 0.0766 0.0825 0.8409 4 R 0.0620 0.0726 0.8654 5 D 0.1188 0.0379 0.8433 6 N 0.3307 0.0524 0.6169 7 K 0.5851 0.0409 0.3740 8 F 0.7497 0.0253 0.2250 9 N 0.8173 0.0180 0.1648 10 T 0.8313 0.0143 0.1544 11 W 0.8262 0.0138 0.1600 12 N 0.6663 0.0140 0.3197 13 D 0.3795 0.0514 0.5691 14 S 0.1280 0.0496 0.8224 15 R 0.0778 0.0485 0.8737 16 G 0.0823 0.0500 0.8677 17 N 0.1899 0.0527 0.7574 18 Y 0.2285 0.0567 0.7149 19 W 0.1616 0.0958 0.7425 20 S 0.1818 0.0795 0.7387 21 D 0.2392 0.0721 0.6888 22 Y 0.2511 0.0365 0.7124 23 E 0.2804 0.0688 0.6508 24 G 0.4379 0.0693 0.4929 25 S 0.6572 0.0428 0.3000 26 D 0.7186 0.0289 0.2525 27 E 0.6760 0.0213 0.3027 28 N 0.4609 0.0331 0.5060 29 G 0.2694 0.0262 0.7044 30 D 0.1846 0.0513 0.7640 31 G 0.3220 0.0330 0.6450 32 I 0.6653 0.0132 0.3215 33 G 0.8647 0.0044 0.1310 34 D 0.9103 0.0033 0.0863 35 S 0.9226 0.0033 0.0741 36 A 0.9283 0.0032 0.0686 37 Y 0.9243 0.0033 0.0724 38 A 0.9171 0.0034 0.0795 39 V 0.8793 0.0042 0.1165 40 N 0.6764 0.0184 0.3052 41 P 0.2638 0.0230 0.7132 42 E 0.0645 0.1174 0.8181 43 A 0.0873 0.0629 0.8498 44 G 0.1336 0.0578 0.8087 45 S 0.2867 0.0387 0.6746 46 M 0.5241 0.0391 0.4368 47 D 0.5601 0.0351 0.4048 48 Y 0.6624 0.0294 0.3082 49 M 0.7345 0.0205 0.2449 50 P 0.7942 0.0142 0.1916 51 L 0.8393 0.0108 0.1499 52 M 0.8587 0.0095 0.1318 53 E 0.8820 0.0063 0.1117 54 Y 0.8687 0.0065 0.1248 55 L 0.7943 0.0097 0.1960 56 H 0.5891 0.0148 0.3961 57 S 0.3181 0.0285 0.6534 58 S 0.1697 0.0471 0.7833 59 P 0.1265 0.0513 0.8223 60 V 0.1436 0.0356 0.8208 61 L 0.1721 0.0265 0.8014 62 P 0.3361 0.0216 0.6423 63 T 0.6315 0.0229 0.3457 64 A 0.7463 0.0181 0.2356 65 R 0.7578 0.0173 0.2249 66 F 0.7774 0.0172 0.2054 67 T 0.7576 0.0218 0.2206 68 S 0.6629 0.0229 0.3142 69 D 0.4230 0.0215 0.5555 70 I 0.2181 0.0857 0.6962 71 T 0.1348 0.0843 0.7809 72 E 0.1537 0.0712 0.7752 73 G 0.1841 0.0547 0.7612 74 F 0.3065 0.0448 0.6487 75 A 0.3876 0.0280 0.5844 76 P 0.4206 0.0267 0.5527 77 L 0.6470 0.0242 0.3288 78 S 0.7960 0.0131 0.1909 79 V 0.8442 0.0076 0.1482 80 R 0.8627 0.0058 0.1314 81 F 0.7957 0.0089 0.1954 82 K 0.6282 0.0144 0.3574 83 D 0.2553 0.0239 0.7208 84 F 0.0583 0.1172 0.8245 85 S 0.0770 0.0329 0.8901 86 E 0.0820 0.0343 0.8837 87 N 0.1878 0.0152 0.7970 88 A 0.5697 0.0212 0.4092 89 T 0.7773 0.0172 0.2055 90 S 0.8676 0.0096 0.1228 91 R 0.8734 0.0086 0.1180 92 L 0.8827 0.0071 0.1102 93 W 0.8805 0.0075 0.1120 94 M 0.7837 0.0088 0.2075 95 F 0.4835 0.0412 0.4753 96 G 0.1593 0.0459 0.7948 97 D 0.0857 0.0475 0.8668 98 G 0.0725 0.0521 0.8754 99 N 0.2056 0.0404 0.7540 100 T 0.2710 0.0486 0.6804 101 S 0.2055 0.0641 0.7304 102 D 0.1601 0.0885 0.7514 103 S 0.1687 0.0638 0.7675 104 P 0.2218 0.0489 0.7293 105 S 0.2339 0.0232 0.7430 106 P 0.2768 0.0476 0.6756 107 L 0.5075 0.0491 0.4434 108 H 0.7679 0.0249 0.2072 109 T 0.8174 0.0160 0.1666 110 F 0.7801 0.0129 0.2070 111 F 0.5604 0.0227 0.4169 112 N 0.3153 0.0175 0.6672 113 E 0.1938 0.0428 0.7633 114 G 0.3131 0.0241 0.6628 115 E 0.6536 0.0097 0.3368 116 Y 0.8682 0.0042 0.1276 117 I 0.9139 0.0033 0.0828 118 V 0.9235 0.0033 0.0732 119 S 0.9295 0.0031 0.0674 120 L 0.9256 0.0034 0.0711 121 I 0.9224 0.0033 0.0743 122 V 0.8912 0.0041 0.1047 123 S 0.7429 0.0166 0.2406 124 N 0.2522 0.0145 0.7333 125 E 0.0325 0.1173 0.8502 126 N 0.0591 0.0296 0.9113 127 D 0.0746 0.0354 0.8900 128 S 0.2348 0.0235 0.7417 129 D 0.5407 0.0199 0.4394 130 S 0.5893 0.0220 0.3887 131 A 0.7560 0.0143 0.2297 132 S 0.8169 0.0123 0.1708 133 V 0.8131 0.0115 0.1754 134 T 0.8244 0.0092 0.1664 135 I 0.7641 0.0119 0.2241 136 R 0.6550 0.0097 0.3353 137 A 0.0972 0.0083 0.8945