# This file is the result of combining several RDB files, specifically # T0386.t04.dssp-ebghstl.rdb (weight 1.53986) # T0386.t04.stride-ebghtl.rdb (weight 1.24869) # T0386.t04.str2.rdb (weight 1.54758) # T0386.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 T0386.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t04.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t04.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t04.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0146 0.4943 0.4911 2 L 0.0091 0.8317 0.1592 3 K 0.0048 0.9479 0.0473 4 E 0.0051 0.9530 0.0419 5 F 0.0051 0.9531 0.0418 6 M 0.0055 0.9511 0.0435 7 H 0.0054 0.9443 0.0503 8 T 0.0066 0.9237 0.0697 9 M 0.0121 0.8767 0.1112 10 K 0.0148 0.8096 0.1755 11 N 0.0240 0.6226 0.3534 12 T 0.0447 0.3421 0.6131 13 G 0.0513 0.0751 0.8737 14 R 0.1394 0.0625 0.7981 15 N 0.2434 0.0697 0.6868 16 V 0.1835 0.2166 0.5999 17 N 0.1556 0.1086 0.7358 18 D 0.1208 0.0765 0.8027 19 R 0.2999 0.0188 0.6813 20 P 0.6196 0.0117 0.3687 21 V 0.8588 0.0090 0.1323 22 M 0.9108 0.0067 0.0824 23 V 0.9069 0.0085 0.0847 24 A 0.8336 0.0161 0.1503 25 K 0.6455 0.0282 0.3263 26 E 0.2051 0.0527 0.7422 27 G 0.1267 0.0357 0.8375 28 E 0.4375 0.0199 0.5426 29 T 0.7836 0.0144 0.2019 30 Y 0.7381 0.0186 0.2433 31 T 0.5359 0.0581 0.4059 32 G 0.5048 0.0496 0.4455 33 T 0.6033 0.0670 0.3297 34 Y 0.6162 0.0739 0.3099 35 R 0.4414 0.1145 0.4441 36 G 0.2599 0.0879 0.6522 37 A 0.2358 0.1191 0.6452 38 G 0.2574 0.1109 0.6317 39 L 0.3110 0.1200 0.5690 40 E 0.3652 0.1020 0.5328 41 G 0.6880 0.0387 0.2733 42 F 0.8663 0.0117 0.1221 43 A 0.9071 0.0088 0.0840 44 L 0.9047 0.0082 0.0872 45 N 0.8784 0.0068 0.1148 46 V 0.7843 0.0118 0.2039 47 K 0.3675 0.0476 0.5849 48 G 0.2410 0.0300 0.7290 49 A 0.6691 0.0128 0.3180 50 Y 0.8744 0.0049 0.1207 51 I 0.8856 0.0045 0.1099 52 I 0.7209 0.0198 0.2592 53 G 0.3726 0.0257 0.6017 54 N 0.2633 0.0417 0.6949 55 I 0.0394 0.5682 0.3925 56 D 0.0237 0.5142 0.4621 57 H 0.0273 0.4491 0.5236 58 L 0.1044 0.0302 0.8654 59 P 0.0714 0.0152 0.9134 60 P 0.0126 0.8113 0.1761 61 E 0.0254 0.7913 0.1833 62 Q 0.0478 0.7872 0.1651 63 L 0.2608 0.4534 0.2857 64 K 0.3784 0.2700 0.3515 65 I 0.5057 0.1796 0.3147 66 L 0.3400 0.0704 0.5896 67 K 0.1224 0.0234 0.8541 68 P 0.0390 0.0818 0.8791 69 G 0.0319 0.0425 0.9256 70 D 0.2231 0.0243 0.7525 71 K 0.6683 0.0147 0.3170 72 I 0.8412 0.0082 0.1505 73 T 0.8491 0.0079 0.1431 74 F 0.6546 0.0092 0.3363 75 T 0.2660 0.0168 0.7172