# This file is the result of combining several RDB files, specifically # T0343.t06.dssp-ebghstl.rdb (weight 1.53986) # T0343.t06.stride-ebghtl.rdb (weight 1.24869) # T0343.t06.str2.rdb (weight 1.54758) # T0343.t06.alpha.rdb (weight 0.659012) # T0343.t04.dssp-ebghstl.rdb (weight 1.53986) # T0343.t04.stride-ebghtl.rdb (weight 1.24869) # T0343.t04.str2.rdb (weight 1.54758) # T0343.t04.alpha.rdb (weight 0.659012) # T0343.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0343.t2k.stride-ebghtl.rdb (weight 1.24869) # T0343.t2k.str2.rdb (weight 1.54758) # T0343.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 T0343.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 # # ============================================ # Comments from T0343.t06.stride-ebghtl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 # # ============================================ # Comments from T0343.t06.str2.rdb # ============================================ # TARGET T0343 # 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 T0343.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 # # ============================================ # Comments from T0343.t06.alpha.rdb # ============================================ # TARGET T0343 # 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 T0343.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 # # ============================================ # Comments from T0343.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.stride-ebghtl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.str2.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.alpha.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t2k.str2.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t2k.alpha.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0661 0.0894 0.8445 2 T 0.1099 0.2370 0.6530 3 W 0.0237 0.8178 0.1585 4 R 0.0079 0.8977 0.0944 5 E 0.0102 0.9170 0.0728 6 I 0.0103 0.9174 0.0723 7 L 0.0175 0.8897 0.0928 8 R 0.0178 0.8585 0.1237 9 K 0.0189 0.7736 0.2074 10 E 0.0473 0.4090 0.5437 11 G 0.0545 0.1233 0.8222 12 F 0.1879 0.1121 0.6999 13 L 0.5282 0.0858 0.3860 14 D 0.5389 0.0736 0.3875 15 L 0.4561 0.1024 0.4415 16 G 0.2491 0.0937 0.6573 17 E 0.3772 0.0638 0.5589 18 F 0.8371 0.0062 0.1567 19 I 0.9145 0.0038 0.0817 20 V 0.9290 0.0032 0.0678 21 E 0.9234 0.0037 0.0728 22 L 0.9239 0.0031 0.0730 23 V 0.9018 0.0040 0.0942 24 Y 0.8350 0.0084 0.1566 25 I 0.5498 0.0493 0.4009 26 D 0.2534 0.0411 0.7056 27 C 0.1504 0.0322 0.8175 28 P 0.1303 0.0557 0.8140 29 C 0.1124 0.0962 0.7913 30 E 0.1030 0.0942 0.8028 31 P 0.1323 0.0714 0.7964 32 I 0.1452 0.0292 0.8256 33 P 0.1130 0.0180 0.8690 34 P 0.2125 0.0218 0.7657 35 T 0.6840 0.0181 0.2978 36 L 0.8852 0.0071 0.1077 37 A 0.9162 0.0042 0.0795 38 I 0.9112 0.0057 0.0831 39 Y 0.8695 0.0078 0.1227 40 D 0.6151 0.0161 0.3688 41 K 0.1492 0.0886 0.7622 42 K 0.0886 0.0793 0.8320 43 G 0.0984 0.0776 0.8241 44 D 0.1559 0.0561 0.7880 45 E 0.5764 0.0469 0.3767 46 W 0.8005 0.0223 0.1772 47 Y 0.8248 0.0187 0.1564 48 K 0.8406 0.0160 0.1433 49 V 0.6823 0.0415 0.2762 50 E 0.4242 0.0900 0.4859 51 E 0.2322 0.0707 0.6971 52 A 0.1658 0.0425 0.7917 53 P 0.1178 0.0824 0.7999 54 N 0.1018 0.1087 0.7895 55 V 0.1052 0.1725 0.7223 56 Q 0.0823 0.1989 0.7188 57 N 0.1061 0.2293 0.6646 58 Y 0.0325 0.7108 0.2567 59 R 0.0151 0.8478 0.1371 60 E 0.0111 0.8904 0.0986 61 A 0.0091 0.9009 0.0900 62 V 0.0055 0.9327 0.0618 63 E 0.0052 0.9415 0.0533 64 W 0.0051 0.9423 0.0525 65 A 0.0057 0.9469 0.0474 66 I 0.0054 0.9551 0.0394 67 E 0.0059 0.9552 0.0388 68 V 0.0059 0.9546 0.0395 69 L 0.0064 0.9544 0.0391 70 E 0.0073 0.9506 0.0421 71 R 0.0097 0.9353 0.0549 72 I 0.0179 0.8917 0.0905 73 R 0.0476 0.7296 0.2228 74 D 0.0606 0.3570 0.5824 75 G 0.0400 0.0971 0.8629 76 E 0.0793 0.0902 0.8306 77 N 0.2432 0.0557 0.7011 78 V 0.4975 0.0177 0.4848 79 K 0.7291 0.0105 0.2604 80 L 0.8734 0.0052 0.1214 81 V 0.8336 0.0094 0.1569 82 S 0.7628 0.0078 0.2293 83 L 0.4857 0.0280 0.4863 84 D 0.1530 0.0299 0.8171 85 G 0.0832 0.0300 0.8868 86 P 0.0741 0.0577 0.8681 87 A 0.0751 0.0541 0.8709 88 P 0.0558 0.1172 0.8270 89 P 0.0291 0.5672 0.4037 90 K 0.0149 0.8231 0.1620 91 V 0.0095 0.8903 0.1002 92 M 0.0086 0.9165 0.0749 93 K 0.0071 0.9205 0.0724 94 R 0.0078 0.9116 0.0807 95 L 0.0074 0.9165 0.0761 96 S 0.0070 0.9145 0.0785 97 L 0.0080 0.8899 0.1021 98 A 0.0086 0.8754 0.1160 99 L 0.0117 0.8410 0.1473 100 Q 0.0103 0.7772 0.2125 101 K 0.0160 0.7072 0.2769 102 L 0.0414 0.4712 0.4874 103 T 0.0512 0.2575 0.6912 104 E 0.0268 0.0663 0.9069