# This file is the result of combining several RDB files, specifically # T0309.t06.dssp-ebghstl.rdb (weight 1.53986) # T0309.t06.stride-ebghtl.rdb (weight 1.24869) # T0309.t06.str2.rdb (weight 1.54758) # T0309.t06.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 T0309.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.t06-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 1 # # ============================================ # Comments from T0309.t06.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.t06-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 1 # # ============================================ # Comments from T0309.t06.str2.rdb # ============================================ # TARGET T0309 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0309.t06-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 1 # # ============================================ # Comments from T0309.t06.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.t06-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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0810 0.3376 0.5814 2 A 0.1093 0.3066 0.5840 3 S 0.1144 0.2816 0.6040 4 K 0.1672 0.2634 0.5695 5 K 0.3175 0.1989 0.4836 6 V 0.4580 0.1535 0.3885 7 H 0.5409 0.1327 0.3264 8 Q 0.6903 0.0853 0.2244 9 I 0.6695 0.0639 0.2665 10 N 0.6289 0.0497 0.3214 11 V 0.5750 0.0808 0.3442 12 K 0.3806 0.1326 0.4868 13 G 0.3250 0.1157 0.5593 14 F 0.4605 0.1061 0.4334 15 F 0.4901 0.0711 0.4388 16 D 0.3880 0.0582 0.5538 17 M 0.3137 0.1306 0.5558 18 D 0.4053 0.1326 0.4621 19 V 0.4780 0.2321 0.2898 20 M 0.5648 0.1926 0.2427 21 E 0.6282 0.1653 0.2065 22 V 0.5053 0.1979 0.2968 23 T 0.3848 0.1970 0.4182 24 E 0.2468 0.3351 0.4182 25 Q 0.1826 0.3560 0.4614 26 T 0.1641 0.2517 0.5842 27 K 0.1426 0.3574 0.4999 28 E 0.1698 0.4183 0.4119 29 A 0.2046 0.3992 0.3963 30 E 0.2696 0.3297 0.4007 31 Y 0.3243 0.2560 0.4196 32 T 0.2845 0.2251 0.4904 33 Y 0.2224 0.1876 0.5900 34 D 0.1794 0.1898 0.6308 35 F 0.0189 0.8980 0.0832 36 K 0.0152 0.9266 0.0582 37 E 0.0199 0.9228 0.0573 38 I 0.0278 0.9079 0.0643 39 L 0.0250 0.8934 0.0816 40 S 0.0243 0.8532 0.1225 41 E 0.0279 0.7680 0.2041 42 F 0.0807 0.4469 0.4724 43 N 0.0625 0.1457 0.7918 44 G 0.0508 0.0648 0.8843 45 K 0.1416 0.0622 0.7963 46 N 0.4356 0.0317 0.5328 47 V 0.6754 0.0114 0.3132 48 S 0.7878 0.0086 0.2035 49 I 0.8566 0.0059 0.1375 50 T 0.8581 0.0082 0.1337 51 V 0.8023 0.0156 0.1821 52 K 0.6738 0.0362 0.2900 53 E 0.5169 0.0976 0.3856 54 E 0.3082 0.1726 0.5192 55 N 0.2173 0.1376 0.6451 56 E 0.2927 0.0848 0.6225 57 L 0.3532 0.0263 0.6205 58 P 0.3292 0.0418 0.6290 59 V 0.3691 0.0932 0.5377 60 K 0.2122 0.1587 0.6291 61 G 0.2307 0.1192 0.6501 62 V 0.5048 0.0842 0.4109 63 E 0.6325 0.0794 0.2881 64 M 0.5295 0.1146 0.3559 65 A 0.2702 0.0986 0.6312 66 G 0.1018 0.0559 0.8423