# This file is the result of combining several RDB files, specifically # TR469.t04.str2.rdb (weight 1.54425) # TR469.t04.str4.rdb (weight 0.924988) # TR469.t04.pb.rdb (weight 0.789901) # TR469.t04.bys.rdb (weight 0.748322) # TR469.t04.alpha.rdb (weight 0.678173) # 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 TR469.t04.str2.rdb # ============================================ # TARGET TR469 # Using neural net dunbrack-40pc-3157-t04-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 TR469.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 19.6664 # # ============================================ # Comments from TR469.t04.str4.rdb # ============================================ # TARGET TR469 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR469.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 19.6664 # # ============================================ # Comments from TR469.t04.pb.rdb # ============================================ # TARGET TR469 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR469.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 19.6664 # # ============================================ # Comments from TR469.t04.bys.rdb # ============================================ # TARGET TR469 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR469.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 19.6664 # # ============================================ # Comments from TR469.t04.alpha.rdb # ============================================ # TARGET TR469 # Using neural net dunbrack-40pc-3157-t04-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 TR469.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 19.6664 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Q 0.2470 0.1306 0.6224 2 K 0.3094 0.1224 0.5681 3 F 0.3286 0.0880 0.5835 4 T 0.2033 0.0811 0.7156 5 K 0.0691 0.4411 0.4897 6 D 0.0793 0.3687 0.5519 7 M 0.2050 0.2600 0.5350 8 T 0.1919 0.3002 0.5079 9 F 0.0330 0.7598 0.2071 10 A 0.0140 0.8580 0.1280 11 Q 0.0121 0.9087 0.0792 12 A 0.0145 0.8914 0.0941 13 L 0.0193 0.8544 0.1263 14 Q 0.0246 0.7802 0.1952 15 T 0.0417 0.6105 0.3478 16 H 0.1408 0.2665 0.5927 17 P 0.0260 0.6437 0.3303 18 G 0.0248 0.6079 0.3673 19 V 0.0474 0.6935 0.2590 20 A 0.0357 0.7969 0.1674 21 G 0.0306 0.8538 0.1156 22 V 0.0366 0.8681 0.0953 23 L 0.0347 0.8569 0.1084 24 R 0.0336 0.8421 0.1242 25 S 0.0411 0.7328 0.2261 26 Y 0.0804 0.3821 0.5375 27 N 0.0784 0.1547 0.7669 28 L 0.1459 0.1560 0.6981 29 G 0.1629 0.1525 0.6846 30 C 0.2020 0.1935 0.6045 31 I 0.1839 0.2066 0.6095 32 G 0.1864 0.1414 0.6722 33 C 0.2070 0.1497 0.6433 34 M 0.1468 0.3338 0.5194 35 G 0.1262 0.3893 0.4844 36 A 0.1195 0.4605 0.4200 37 Q 0.0874 0.5184 0.3942 38 N 0.0698 0.5952 0.3351 39 E 0.0775 0.6528 0.2697 40 S 0.0951 0.6494 0.2555 41 L 0.0164 0.8461 0.1375 42 E 0.0103 0.8843 0.1054 43 Q 0.0093 0.9083 0.0824 44 G 0.0120 0.9028 0.0853 45 A 0.0131 0.8738 0.1132 46 N 0.0146 0.8513 0.1341 47 A 0.0240 0.7221 0.2539 48 H 0.0602 0.2411 0.6988 49 G 0.0590 0.1158 0.8252 50 L 0.1685 0.0900 0.7414 51 N 0.1795 0.0230 0.7975 52 V 0.0147 0.7112 0.2740 53 E 0.0093 0.8583 0.1324 54 D 0.0084 0.9121 0.0795 55 I 0.0086 0.9115 0.0799 56 L 0.0084 0.9061 0.0854 57 R 0.0084 0.8797 0.1119 58 D 0.0087 0.8921 0.0991 59 L 0.0106 0.8539 0.1354 60 N 0.0112 0.6520 0.3368 61 A 0.0149 0.5569 0.4282 62 L 0.0463 0.4238 0.5299 63 A 0.0811 0.3223 0.5966