# This file is the result of combining several RDB files, specifically # T0372.t06.dssp-ebghstl.rdb (weight 1.53986) # T0372.t06.stride-ebghtl.rdb (weight 1.24869) # T0372.t06.str2.rdb (weight 1.54758) # T0372.t06.alpha.rdb (weight 0.659012) # T0372.t04.dssp-ebghstl.rdb (weight 1.53986) # T0372.t04.stride-ebghtl.rdb (weight 1.24869) # T0372.t04.str2.rdb (weight 1.54758) # T0372.t04.alpha.rdb (weight 0.659012) # T0372.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0372.t2k.stride-ebghtl.rdb (weight 1.24869) # T0372.t2k.str2.rdb (weight 1.54758) # T0372.t2k.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 T0372.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # Using neural net t06-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 T0372.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 26 # # ============================================ # Comments from T0372.t06.stride-ebghtl.rdb # ============================================ # TARGET T0372 # Using neural net t06-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 T0372.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 26 # # ============================================ # Comments from T0372.t06.str2.rdb # ============================================ # TARGET T0372 # Using neural net 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 T0372.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 26 # # ============================================ # Comments from T0372.t06.alpha.rdb # ============================================ # TARGET T0372 # Using neural net 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 T0372.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 26 # # ============================================ # Comments from T0372.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # Using neural net t06-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 T0372.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 23 # # ============================================ # Comments from T0372.t04.stride-ebghtl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t04.str2.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t04.alpha.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0372.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0372.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0372 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0372.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0372.t2k.str2.rdb # ============================================ # TARGET T0372 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0372.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0372.t2k.alpha.rdb # ============================================ # TARGET T0372 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0372.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0682 0.0306 0.9012 2 I 0.1411 0.0339 0.8249 3 P 0.1541 0.0555 0.7904 4 F 0.1833 0.0359 0.7808 5 K 0.2813 0.0187 0.7001 6 D 0.3779 0.0122 0.6099 7 I 0.3599 0.0128 0.6273 8 T 0.2599 0.0132 0.7269 9 L 0.1561 0.4323 0.4116 10 A 0.0725 0.4650 0.4625 11 D 0.0694 0.4633 0.4673 12 R 0.0092 0.8358 0.1550 13 D 0.0069 0.8531 0.1400 14 T 0.0095 0.8614 0.1292 15 I 0.0101 0.8954 0.0945 16 T 0.0074 0.9229 0.0697 17 A 0.0072 0.9186 0.0742 18 F 0.0075 0.9002 0.0922 19 T 0.0131 0.8519 0.1350 20 M 0.0118 0.7704 0.2178 21 K 0.0171 0.6290 0.3539 22 S 0.0544 0.3520 0.5935 23 D 0.0774 0.1802 0.7424 24 R 0.1325 0.2194 0.6480 25 R 0.2099 0.2321 0.5581 26 N 0.2695 0.2075 0.5230 27 C 0.2660 0.1676 0.5664 28 D 0.1960 0.2202 0.5838 29 L 0.2590 0.2219 0.5192 30 S 0.3689 0.2056 0.4255 31 F 0.3648 0.2872 0.3479 32 S 0.3050 0.3637 0.3313 33 N 0.3126 0.3755 0.3120 34 L 0.3692 0.4050 0.2258 35 C 0.4899 0.3321 0.1780 36 S 0.4728 0.3303 0.1969 37 W 0.3913 0.3531 0.2556 38 R 0.3209 0.3548 0.3243 39 F 0.2643 0.3223 0.4134 40 L 0.2496 0.2668 0.4836 41 Y 0.2170 0.1616 0.6214 42 D 0.2658 0.0606 0.6736 43 T 0.6036 0.0224 0.3740 44 Q 0.8210 0.0104 0.1686 45 F 0.9042 0.0060 0.0898 46 A 0.9103 0.0051 0.0846 47 V 0.9091 0.0065 0.0844 48 I 0.8300 0.0240 0.1461 49 D 0.2012 0.0356 0.7632 50 D 0.1055 0.0628 0.8317 51 F 0.8119 0.0078 0.1803 52 L 0.9229 0.0033 0.0737 53 V 0.9258 0.0039 0.0703 54 F 0.9251 0.0038 0.0711 55 K 0.8788 0.0137 0.1075 56 F 0.8249 0.0079 0.1672 57 W 0.6519 0.0167 0.3314 58 A 0.3755 0.0330 0.5916 59 G 0.0693 0.0784 0.8523 60 E 0.0553 0.0504 0.8943 61 Q 0.1881 0.0274 0.7844 62 L 0.4556 0.0191 0.5254 63 A 0.7226 0.0158 0.2616 64 Y 0.7934 0.0153 0.1913 65 M 0.7141 0.0183 0.2675 66 M 0.5301 0.0172 0.4528 67 P 0.2971 0.0214 0.6815 68 V 0.1395 0.0646 0.7959 69 G 0.0689 0.0782 0.8530 70 N 0.0380 0.1435 0.8184 71 G 0.0342 0.1199 0.8459 72 D 0.0739 0.1436 0.7825 73 L 0.0278 0.7116 0.2606 74 K 0.0132 0.8903 0.0964 75 A 0.0083 0.9263 0.0653 76 V 0.0062 0.9442 0.0497 77 L 0.0052 0.9530 0.0418 78 R 0.0047 0.9569 0.0384 79 K 0.0047 0.9561 0.0391 80 L 0.0047 0.9544 0.0409 81 I 0.0050 0.9517 0.0433 82 E 0.0051 0.9394 0.0555 83 D 0.0052 0.9209 0.0739 84 A 0.0082 0.8823 0.1095 85 D 0.0099 0.8241 0.1661 86 K 0.0183 0.6702 0.3115 87 E 0.0381 0.3384 0.6235 88 K 0.0390 0.1351 0.8259 89 H 0.0808 0.0983 0.8210 90 N 0.1144 0.0760 0.8096 91 F 0.4824 0.0450 0.4726 92 C 0.7311 0.0310 0.2379 93 M 0.7501 0.0294 0.2205 94 L 0.6081 0.0604 0.3316 95 G 0.4289 0.0427 0.5284 96 V 0.1851 0.0230 0.7918 97 C 0.0803 0.0236 0.8961 98 S 0.0096 0.8652 0.1253 99 N 0.0059 0.9179 0.0761 100 M 0.0055 0.9408 0.0537 101 R 0.0051 0.9521 0.0428 102 A 0.0051 0.9511 0.0438 103 D 0.0051 0.9447 0.0503 104 L 0.0056 0.9353 0.0591 105 E 0.0060 0.9250 0.0690 106 A 0.0079 0.8634 0.1287 107 I 0.0184 0.7016 0.2801 108 L 0.0792 0.1775 0.7433 109 P 0.0287 0.1761 0.7952 110 E 0.0345 0.1594 0.8062 111 R 0.2317 0.1150 0.6533 112 F 0.7111 0.0196 0.2693 113 I 0.7891 0.0150 0.1959 114 F 0.7705 0.0211 0.2084 115 T 0.6381 0.0421 0.3198 116 E 0.4634 0.0658 0.4707 117 D 0.2686 0.0801 0.6513 118 R 0.1199 0.1606 0.7195 119 A 0.0929 0.1389 0.7682 120 Y 0.0793 0.1533 0.7674 121 A 0.0643 0.1136 0.8221 122 D 0.0672 0.0308 0.9020