# This file is the result of combining several RDB files, specifically # T0499.t06.str2.rdb (weight 1.54425) # T0499.t06.str4.rdb (weight 0.924988) # T0499.t06.pb.rdb (weight 0.789901) # T0499.t06.bys.rdb (weight 0.748322) # T0499.t06.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 T0499.t06.str2.rdb # ============================================ # TARGET T0499 # Using neural net dunbrack-40pc-3157-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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t06.str4.rdb # ============================================ # TARGET T0499 # Using neural net dunbrack-40pc-3157-t06-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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t06.pb.rdb # ============================================ # TARGET T0499 # Using neural net dunbrack-40pc-3157-t06-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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t06.bys.rdb # ============================================ # TARGET T0499 # Using neural net dunbrack-40pc-3157-t06-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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t06.alpha.rdb # ============================================ # TARGET T0499 # Using neural net dunbrack-40pc-3157-t06-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 T0499.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 3.77849 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.4538 0.0649 0.4813 2 T 0.5943 0.0339 0.3719 3 Y 0.7386 0.0177 0.2436 4 K 0.7950 0.0107 0.1943 5 L 0.8113 0.0066 0.1821 6 I 0.8144 0.0072 0.1783 7 L 0.7972 0.0092 0.1936 8 N 0.6699 0.0222 0.3079 9 L 0.4011 0.1669 0.4320 10 K 0.2164 0.2999 0.4837 11 Q 0.1839 0.3686 0.4476 12 A 0.1521 0.4362 0.4117 13 K 0.1103 0.5595 0.3302 14 E 0.0764 0.6987 0.2249 15 E 0.0748 0.7528 0.1724 16 A 0.0730 0.7573 0.1697 17 I 0.0611 0.7825 0.1563 18 K 0.0534 0.7794 0.1672 19 E 0.0617 0.7606 0.1776 20 A 0.0814 0.6766 0.2420 21 V 0.1755 0.5387 0.2858 22 D 0.1539 0.4349 0.4112 23 A 0.0191 0.7540 0.2269 24 G 0.0116 0.8333 0.1551 25 T 0.0118 0.8844 0.1039 26 A 0.0091 0.9005 0.0904 27 E 0.0085 0.9126 0.0790 28 K 0.0083 0.9198 0.0719 29 Y 0.0084 0.9197 0.0719 30 F 0.0084 0.9177 0.0739 31 K 0.0085 0.9170 0.0746 32 L 0.0099 0.9035 0.0865 33 I 0.0202 0.8464 0.1334 34 A 0.0402 0.7490 0.2108 35 N 0.0628 0.6004 0.3369 36 A 0.0555 0.4119 0.5326 37 K 0.0827 0.2452 0.6721 38 T 0.1852 0.1329 0.6820 39 V 0.3545 0.0830 0.5624 40 E 0.3299 0.0717 0.5984 41 G 0.3973 0.0496 0.5531 42 V 0.5442 0.0484 0.4074 43 W 0.6717 0.0336 0.2947 44 T 0.6190 0.0394 0.3415 45 Y 0.4808 0.0916 0.4275 46 K 0.2652 0.2665 0.4683 47 D 0.2195 0.3258 0.4547 48 E 0.2819 0.2712 0.4469 49 I 0.4387 0.1364 0.4250 50 K 0.5808 0.0749 0.3443 51 T 0.6686 0.0304 0.3010 52 F 0.7059 0.0202 0.2739 53 T 0.6949 0.0151 0.2900 54 V 0.5843 0.0296 0.3861 55 T 0.4412 0.0447 0.5141 56 E 0.3236 0.1179 0.5585