# This file is the result of combining several RDB files, specifically # T0262.t04.dssp-ebghstl.rdb (weight 1.53986) # T0262.t04.stride-ebghtl.rdb (weight 1.24869) # T0262.t04.str2.rdb (weight 1.54758) # T0262.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 T0262.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 4.55178 # # ============================================ # Comments from T0262.t04.stride-ebghtl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 4.55178 # # ============================================ # Comments from T0262.t04.str2.rdb # ============================================ # TARGET T0262 # 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 T0262.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 4.55178 # # ============================================ # Comments from T0262.t04.alpha.rdb # ============================================ # TARGET T0262 # 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 T0262.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 4.55178 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.1074 0.0757 0.8169 2 L 0.1225 0.0753 0.8022 3 T 0.1090 0.0432 0.8477 4 S 0.0755 0.0946 0.8298 5 S 0.0898 0.0559 0.8543 6 L 0.0062 0.9104 0.0834 7 E 0.0048 0.9441 0.0511 8 D 0.0053 0.9418 0.0529 9 A 0.0080 0.9350 0.0570 10 V 0.0155 0.8949 0.0896 11 S 0.0327 0.8113 0.1559 12 T 0.0640 0.6301 0.3059 13 G 0.1012 0.3955 0.5033 14 R 0.1571 0.3508 0.4921 15 R 0.2092 0.2697 0.5211 16 H 0.1208 0.1565 0.7227 17 G 0.0687 0.0729 0.8583 18 N 0.0642 0.0788 0.8569 19 L 0.1952 0.0254 0.7794 20 V 0.4338 0.0076 0.5587 21 A 0.8720 0.0042 0.1239 22 V 0.9259 0.0036 0.0705 23 L 0.9246 0.0070 0.0685 24 L 0.9155 0.0077 0.0768 25 V 0.7958 0.0233 0.1809 26 D 0.3746 0.0359 0.5895 27 V 0.0115 0.8730 0.1155 28 E 0.0055 0.9347 0.0598 29 C 0.0048 0.9479 0.0473 30 L 0.0051 0.9476 0.0473 31 R 0.0050 0.9376 0.0574 32 R 0.0066 0.8703 0.1231 33 R 0.0405 0.3758 0.5837 34 G 0.0374 0.0420 0.9206 35 L 0.1897 0.0221 0.7882 36 K 0.7422 0.0193 0.2385 37 V 0.8380 0.0361 0.1259 38 E 0.7327 0.0675 0.1998 39 R 0.6681 0.0724 0.2594 40 M 0.3517 0.0832 0.5651 41 S 0.2176 0.0297 0.7528 42 K 0.2634 0.0291 0.7075 43 T 0.7009 0.0076 0.2915 44 V 0.8740 0.0037 0.1223 45 Y 0.9055 0.0043 0.0902 46 T 0.9135 0.0043 0.0823 47 V 0.8162 0.0156 0.1682 48 D 0.6803 0.0253 0.2944 49 W 0.4717 0.0262 0.5022 50 V 0.2407 0.0174 0.7420 51 P 0.0980 0.0148 0.8872 52 P 0.0121 0.7891 0.1988 53 E 0.0122 0.8409 0.1468 54 C 0.0148 0.8674 0.1178 55 I 0.0171 0.9038 0.0790 56 A 0.0162 0.9144 0.0694 57 E 0.0205 0.8981 0.0814 58 V 0.0540 0.8263 0.1197 59 R 0.1001 0.6950 0.2049 60 R 0.0997 0.5370 0.3632 61 E 0.0792 0.3097 0.6111 62 S 0.0640 0.2634 0.6726 63 L 0.0819 0.2002 0.7180 64 G 0.0703 0.1269 0.8027 65 R 0.0905 0.1043 0.8052 66 S 0.1095 0.0483 0.8422 67 L 0.0556 0.0853 0.8592