# This file is the result of combining several RDB files, specifically # T0281.t04.dssp-ebghstl.rdb (weight 1.53986) # T0281.t04.stride-ebghtl.rdb (weight 1.24869) # T0281.t04.str2.rdb (weight 1.54758) # T0281.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 T0281.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0281 # 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 T0281.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 21.5106 # # ============================================ # Comments from T0281.t04.stride-ebghtl.rdb # ============================================ # TARGET T0281 # 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 T0281.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 21.5106 # # ============================================ # Comments from T0281.t04.str2.rdb # ============================================ # TARGET T0281 # 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 T0281.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 21.5106 # # ============================================ # Comments from T0281.t04.alpha.rdb # ============================================ # TARGET T0281 # 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 T0281.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 21.5106 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0741 0.0269 0.8991 2 W 0.1007 0.0301 0.8693 3 M 0.0819 0.0152 0.9029 4 P 0.0728 0.0108 0.9164 5 P 0.0821 0.0125 0.9054 6 R 0.0569 0.0167 0.9264 7 P 0.0050 0.9323 0.0627 8 E 0.0047 0.9601 0.0352 9 E 0.0046 0.9613 0.0340 10 V 0.0047 0.9608 0.0346 11 A 0.0046 0.9611 0.0343 12 R 0.0046 0.9615 0.0339 13 K 0.0046 0.9614 0.0339 14 L 0.0047 0.9599 0.0355 15 R 0.0048 0.9531 0.0421 16 R 0.0055 0.9177 0.0768 17 L 0.0407 0.5062 0.4531 18 G 0.0406 0.0867 0.8726 19 F 0.1876 0.0677 0.7447 20 V 0.6436 0.0880 0.2684 21 E 0.7214 0.1067 0.1719 22 R 0.6763 0.1172 0.2065 23 M 0.6160 0.1077 0.2763 24 A 0.5354 0.1071 0.3575 25 K 0.3642 0.1065 0.5294 26 G 0.2582 0.0589 0.6829 27 G 0.2451 0.0958 0.6591 28 H 0.4376 0.1238 0.4386 29 R 0.5702 0.1491 0.2807 30 L 0.6900 0.1145 0.1955 31 Y 0.8089 0.0417 0.1494 32 T 0.8128 0.0226 0.1646 33 H 0.2286 0.0217 0.7497 34 P 0.0265 0.0979 0.8756 35 D 0.0458 0.0234 0.9308 36 G 0.0533 0.0312 0.9155 37 R 0.2709 0.0094 0.7197 38 I 0.8668 0.0037 0.1295 39 V 0.9080 0.0044 0.0876 40 V 0.9077 0.0041 0.0882 41 V 0.8490 0.0064 0.1446 42 P 0.6587 0.0101 0.3312 43 F 0.2624 0.0151 0.7225 44 H 0.1190 0.0296 0.8514 45 S 0.0386 0.2590 0.7024 46 G 0.0239 0.1834 0.7927 47 E 0.0648 0.1973 0.7378 48 L 0.0916 0.0278 0.8806 49 P 0.0571 0.0495 0.8934 50 K 0.0146 0.4910 0.4944 51 G 0.0205 0.5543 0.4251 52 T 0.0287 0.7820 0.1893 53 F 0.0121 0.9277 0.0602 54 K 0.0050 0.9556 0.0394 55 R 0.0047 0.9598 0.0355 56 I 0.0047 0.9614 0.0340 57 L 0.0047 0.9599 0.0354 58 R 0.0051 0.9539 0.0410 59 D 0.0058 0.9252 0.0691 60 A 0.0446 0.5096 0.4458 61 G 0.0425 0.0291 0.9284 62 L 0.0741 0.0096 0.9163 63 T 0.0688 0.0133 0.9179 64 E 0.0078 0.8970 0.0952 65 E 0.0064 0.9189 0.0746 66 E 0.0066 0.9151 0.0782 67 F 0.0133 0.8730 0.1137 68 H 0.0233 0.6839 0.2928 69 N 0.0290 0.4003 0.5707 70 L 0.0298 0.0959 0.8743