# This file is the result of combining several RDB files, specifically # T0242.t04.dssp-ebghstl.rdb (weight 1.53986) # T0242.t04.stride-ebghtl.rdb (weight 1.24869) # T0242.t04.str2.rdb (weight 1.54758) # T0242.t04.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 T0242.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0242 # 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 T0242.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 3.68025 # # ============================================ # Comments from T0242.t04.stride-ebghtl.rdb # ============================================ # TARGET T0242 # 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 T0242.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 3.68025 # # ============================================ # Comments from T0242.t04.str2.rdb # ============================================ # TARGET T0242 # 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 T0242.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 3.68025 # # ============================================ # Comments from T0242.t04.alpha.rdb # ============================================ # TARGET T0242 # 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 T0242.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 3.68025 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1148 0.0902 0.7950 2 G 0.1401 0.0731 0.7868 3 K 0.5094 0.0702 0.4204 4 V 0.8209 0.0322 0.1469 5 F 0.8675 0.0349 0.0975 6 L 0.8629 0.0332 0.1040 7 T 0.7212 0.0676 0.2111 8 N 0.4840 0.0815 0.4345 9 A 0.3300 0.1425 0.5275 10 F 0.3233 0.1410 0.5357 11 S 0.2131 0.2391 0.5478 12 I 0.0231 0.8100 0.1669 13 N 0.0182 0.8373 0.1445 14 M 0.0157 0.8455 0.1388 15 L 0.0249 0.7544 0.2207 16 K 0.0250 0.5887 0.3862 17 E 0.0312 0.3027 0.6661 18 F 0.0751 0.0308 0.8941 19 P 0.0803 0.0465 0.8732 20 T 0.3459 0.0488 0.6054 21 T 0.8227 0.0233 0.1540 22 I 0.8927 0.0105 0.0968 23 T 0.8660 0.0108 0.1233 24 I 0.6863 0.0653 0.2484 25 D 0.3118 0.1323 0.5559 26 K 0.2230 0.1394 0.6376 27 L 0.2500 0.0431 0.7068 28 D 0.1218 0.0519 0.8263 29 E 0.0180 0.7860 0.1960 30 E 0.0197 0.8310 0.1493 31 D 0.0226 0.8519 0.1255 32 F 0.0421 0.8292 0.1287 33 C 0.0829 0.7597 0.1574 34 L 0.1330 0.6558 0.2111 35 K 0.2025 0.4941 0.3033 36 L 0.3404 0.2900 0.3696 37 E 0.4467 0.2136 0.3396 38 L 0.5696 0.1303 0.3000 39 R 0.5558 0.1049 0.3392 40 L 0.3047 0.1367 0.5586 41 E 0.1324 0.1327 0.7350 42 D 0.0719 0.0729 0.8552 43 G 0.0690 0.0978 0.8331 44 T 0.2960 0.0985 0.6055 45 L 0.6428 0.1584 0.1988 46 I 0.6083 0.2185 0.1732 47 N 0.4842 0.3104 0.2053 48 A 0.3605 0.3779 0.2616 49 I 0.2415 0.3339 0.4246 50 G 0.1247 0.2210 0.6544 51 H 0.0390 0.6252 0.3359 52 D 0.0077 0.9255 0.0669 53 S 0.0051 0.9437 0.0512 54 T 0.0048 0.9529 0.0423 55 I 0.0047 0.9595 0.0358 56 N 0.0047 0.9572 0.0381 57 L 0.0053 0.9534 0.0413 58 V 0.0050 0.9500 0.0450 59 N 0.0055 0.9442 0.0502 60 T 0.0074 0.9213 0.0713 61 L 0.0117 0.8876 0.1008 62 C 0.0394 0.7132 0.2474 63 G 0.0395 0.4404 0.5200 64 T 0.1032 0.3701 0.5267 65 Q 0.2155 0.3236 0.4609 66 L 0.2192 0.3364 0.4444 67 Q 0.2097 0.3356 0.4547 68 K 0.3087 0.2447 0.4466 69 N 0.4655 0.0524 0.4821 70 R 0.7683 0.0171 0.2147 71 V 0.8815 0.0054 0.1131 72 E 0.9102 0.0051 0.0848 73 V 0.9036 0.0045 0.0919 74 K 0.8730 0.0044 0.1226 75 M 0.6637 0.0136 0.3227 76 N 0.2377 0.0281 0.7342 77 E 0.0513 0.0727 0.8761 78 G 0.0519 0.0512 0.8969 79 D 0.1842 0.0313 0.7845 80 E 0.6564 0.0340 0.3096 81 A 0.8902 0.0058 0.1040 82 L 0.9162 0.0053 0.0786 83 I 0.9264 0.0059 0.0676 84 I 0.9188 0.0086 0.0726 85 M 0.8989 0.0209 0.0802 86 I 0.7882 0.0884 0.1234 87 S 0.5513 0.2223 0.2264 88 Q 0.4717 0.2781 0.2502 89 R 0.3939 0.3288 0.2773 90 L 0.2590 0.3424 0.3986 91 E 0.1866 0.3247 0.4887 92 E 0.0870 0.2051 0.7079 93 G 0.0654 0.0837 0.8508 94 K 0.2575 0.0636 0.6789 95 V 0.6216 0.0329 0.3455 96 L 0.3648 0.0184 0.6169 97 S 0.1339 0.0119 0.8542 98 D 0.0058 0.9344 0.0598 99 K 0.0047 0.9599 0.0355 100 E 0.0047 0.9596 0.0357 101 I 0.0047 0.9589 0.0364 102 K 0.0047 0.9568 0.0385 103 D 0.0053 0.9481 0.0466 104 M 0.0075 0.9339 0.0586 105 Y 0.0172 0.8451 0.1377 106 R 0.0184 0.6559 0.3257 107 Q 0.0444 0.1648 0.7908 108 G 0.0321 0.0322 0.9357 109 K 0.2804 0.0217 0.6979 110 I 0.7695 0.0040 0.2264 111 S 0.8382 0.0073 0.1545 112 F 0.9107 0.0060 0.0832 113 Y 0.8990 0.0090 0.0920 114 E 0.8970 0.0058 0.0972 115 V 0.7375 0.0131 0.2494 116 W 0.3344 0.0187 0.6469