# This file is the result of combining several RDB files, specifically # T0311.t04.dssp-ebghstl.rdb (weight 1.53986) # T0311.t04.stride-ebghtl.rdb (weight 1.24869) # T0311.t04.str2.rdb (weight 1.54758) # T0311.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 T0311.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0311 # Using neural net t06-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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.stride-ebghtl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.str2.rdb # ============================================ # TARGET T0311 # Using neural net t06-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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.alpha.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0712 0.0247 0.9041 2 K 0.1445 0.0465 0.8090 3 M 0.1578 0.0878 0.7544 4 A 0.1365 0.0820 0.7816 5 N 0.1148 0.0439 0.8414 6 H 0.0834 0.0154 0.9012 7 P 0.0988 0.0150 0.8862 8 R 0.0783 0.0207 0.9010 9 P 0.0253 0.6362 0.3384 10 G 0.0214 0.7218 0.2568 11 D 0.0413 0.8225 0.1362 12 I 0.0363 0.8583 0.1054 13 I 0.0192 0.8901 0.0907 14 Q 0.0116 0.9025 0.0859 15 E 0.0106 0.8764 0.1130 16 S 0.0106 0.8555 0.1339 17 L 0.0285 0.8270 0.1445 18 D 0.0099 0.8315 0.1586 19 E 0.0092 0.7736 0.2172 20 L 0.0487 0.3504 0.6009 21 N 0.0483 0.0509 0.9008 22 V 0.0877 0.0175 0.8949 23 S 0.1184 0.0247 0.8569 24 L 0.0048 0.9466 0.0486 25 R 0.0047 0.9595 0.0359 26 E 0.0047 0.9602 0.0352 27 F 0.0046 0.9611 0.0342 28 A 0.0047 0.9579 0.0373 29 R 0.0049 0.9440 0.0511 30 A 0.0054 0.8915 0.1031 31 M 0.0485 0.4629 0.4886 32 E 0.0407 0.0440 0.9153 33 I 0.0704 0.0159 0.9137 34 A 0.0610 0.0131 0.9259 35 P 0.0090 0.9005 0.0905 36 S 0.0070 0.9272 0.0658 37 T 0.0063 0.9367 0.0570 38 A 0.0048 0.9538 0.0414 39 S 0.0050 0.9542 0.0408 40 R 0.0056 0.9495 0.0450 41 L 0.0058 0.9450 0.0492 42 L 0.0103 0.8978 0.0919 43 T 0.0357 0.5158 0.4485 44 G 0.0298 0.2005 0.7697 45 K 0.0738 0.1821 0.7441 46 A 0.1269 0.1667 0.7063 47 A 0.1560 0.1049 0.7390 48 L 0.1634 0.0452 0.7913 49 T 0.0686 0.0418 0.8896 50 P 0.0047 0.9532 0.0421 51 E 0.0047 0.9600 0.0353 52 M 0.0047 0.9586 0.0367 53 A 0.0047 0.9603 0.0351 54 I 0.0047 0.9595 0.0359 55 K 0.0047 0.9559 0.0394 56 L 0.0048 0.9521 0.0431 57 S 0.0057 0.9456 0.0487 58 V 0.0062 0.9383 0.0555 59 V 0.0122 0.8781 0.1098 60 I 0.0486 0.5604 0.3910 61 G 0.0352 0.1036 0.8612 62 S 0.0675 0.0453 0.8872 63 S 0.0612 0.0344 0.9044 64 P 0.0052 0.9218 0.0730 65 Q 0.0057 0.9400 0.0543 66 M 0.0068 0.9430 0.0502 67 W 0.0099 0.9414 0.0487 68 L 0.0107 0.9279 0.0614 69 N 0.0115 0.8950 0.0935 70 L 0.0111 0.8881 0.1008 71 Q 0.0131 0.8726 0.1142 72 N 0.0127 0.8137 0.1737 73 A 0.0102 0.8332 0.1566 74 W 0.0374 0.7232 0.2394 75 S 0.0456 0.6427 0.3116 76 L 0.0069 0.9264 0.0667 77 A 0.0072 0.9431 0.0497 78 E 0.0099 0.9408 0.0493 79 A 0.0102 0.9337 0.0560 80 E 0.0132 0.9058 0.0811 81 K 0.0119 0.8314 0.1566 82 T 0.0177 0.7228 0.2595 83 V 0.0494 0.5744 0.3763 84 D 0.0687 0.3154 0.6159 85 V 0.0366 0.6228 0.3406 86 S 0.0551 0.6858 0.2591 87 R 0.0998 0.6690 0.2313 88 L 0.1502 0.5645 0.2853 89 R 0.2223 0.4839 0.2938 90 R 0.3396 0.3788 0.2817 91 L 0.3628 0.2770 0.3602 92 V 0.3597 0.2447 0.3956 93 T 0.2913 0.2186 0.4901 94 Q 0.2045 0.1295 0.6660 95 S 0.1248 0.0854 0.7898 96 T 0.0722 0.0252 0.9026 97 P 0.0466 0.0303 0.9231