# This file is the result of combining several RDB files, specifically # T0437.t04.dssp-ebghstl.rdb (weight 1.53986) # T0437.t04.stride-ebghtl.rdb (weight 1.24869) # T0437.t04.str2.rdb (weight 1.54758) # T0437.t04.alpha.rdb (weight 0.659012) # T0437.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0437.t2k.stride-ebghtl.rdb (weight 1.24869) # T0437.t2k.str2.rdb (weight 1.54758) # T0437.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 T0437.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.stride-ebghtl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.str2.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.alpha.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 52 # # ============================================ # Comments from T0437.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 52 # # ============================================ # Comments from T0437.t2k.str2.rdb # ============================================ # TARGET T0437 # 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 T0437.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 52 # # ============================================ # Comments from T0437.t2k.alpha.rdb # ============================================ # TARGET T0437 # 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 T0437.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 52 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0522 0.0722 0.8756 2 K 0.0917 0.1651 0.7431 3 D 0.1248 0.1956 0.6797 4 V 0.0980 0.2066 0.6953 5 V 0.0977 0.1846 0.7177 6 D 0.0818 0.5341 0.3841 7 K 0.0929 0.5623 0.3448 8 C 0.1137 0.5492 0.3371 9 S 0.1261 0.4205 0.4534 10 T 0.1026 0.3206 0.5768 11 K 0.1058 0.1828 0.7114 12 G 0.1273 0.1259 0.7468 13 C 0.2385 0.1125 0.6490 14 A 0.4409 0.1074 0.4517 15 I 0.5322 0.0844 0.3834 16 D 0.6778 0.0415 0.2808 17 I 0.6632 0.0626 0.2742 18 G 0.6944 0.0541 0.2515 19 T 0.8154 0.0328 0.1519 20 V 0.8427 0.0280 0.1293 21 I 0.8009 0.0263 0.1727 22 D 0.4968 0.0252 0.4780 23 N 0.1188 0.0978 0.7835 24 D 0.0814 0.0884 0.8302 25 N 0.1800 0.0485 0.7715 26 C 0.4648 0.0307 0.5045 27 T 0.8353 0.0091 0.1557 28 S 0.8967 0.0049 0.0984 29 K 0.9185 0.0035 0.0781 30 F 0.9071 0.0048 0.0881 31 S 0.9098 0.0040 0.0862 32 R 0.8826 0.0108 0.1066 33 F 0.8171 0.0127 0.1702 34 F 0.5820 0.0140 0.4040 35 A 0.1509 0.0483 0.8008 36 T 0.0840 0.0287 0.8873 37 R 0.0070 0.8481 0.1449 38 E 0.0061 0.9342 0.0598 39 E 0.0056 0.9472 0.0472 40 A 0.0048 0.9543 0.0409 41 E 0.0049 0.9557 0.0394 42 S 0.0048 0.9538 0.0414 43 F 0.0052 0.9511 0.0438 44 M 0.0048 0.9538 0.0414 45 T 0.0049 0.9541 0.0410 46 K 0.0049 0.9496 0.0456 47 L 0.0049 0.9495 0.0456 48 K 0.0049 0.9565 0.0386 49 E 0.0050 0.9490 0.0460 50 L 0.0051 0.9421 0.0528 51 A 0.0059 0.9236 0.0705 52 A 0.0066 0.9139 0.0795 53 A 0.0103 0.8583 0.1314 54 A 0.0334 0.6379 0.3287 55 S 0.0736 0.2231 0.7033 56 S 0.0148 0.3423 0.6429 57 A 0.0210 0.2872 0.6918 58 D 0.0649 0.1891 0.7460 59 E 0.0999 0.0970 0.8032 60 G 0.1948 0.0921 0.7131 61 A 0.4056 0.0832 0.5112 62 S 0.6293 0.0438 0.3268 63 V 0.7289 0.0241 0.2470 64 A 0.7402 0.0224 0.2374 65 Y 0.7343 0.0287 0.2370 66 K 0.8183 0.0160 0.1657 67 I 0.8432 0.0096 0.1471 68 K 0.7526 0.0127 0.2348 69 D 0.7202 0.0283 0.2515 70 L 0.4285 0.0748 0.4968 71 E 0.2008 0.1046 0.6946 72 G 0.1036 0.0589 0.8376 73 Q 0.3431 0.0293 0.6276 74 V 0.8052 0.0051 0.1897 75 E 0.9035 0.0033 0.0931 76 L 0.9005 0.0036 0.0959 77 D 0.9110 0.0031 0.0859 78 A 0.9082 0.0038 0.0880 79 A 0.9203 0.0033 0.0764 80 F 0.9177 0.0037 0.0786 81 T 0.9154 0.0037 0.0809 82 F 0.8568 0.0067 0.1366 83 S 0.8104 0.0134 0.1762 84 C 0.5790 0.0502 0.3709 85 Q 0.4721 0.1173 0.4106 86 A 0.3732 0.4032 0.2237 87 E 0.2853 0.5768 0.1379 88 M 0.2559 0.6495 0.0946 89 I 0.2071 0.7141 0.0788 90 I 0.1582 0.7616 0.0801 91 F 0.1092 0.7943 0.0965 92 E 0.0695 0.8218 0.1087 93 L 0.0455 0.7979 0.1566 94 S 0.0417 0.7292 0.2291 95 L 0.0495 0.6480 0.3025 96 R 0.0341 0.6142 0.3516 97 S 0.0592 0.4516 0.4892 98 L 0.0354 0.3397 0.6249 99 A 0.0252 0.1103 0.8645