# This file is the result of combining several RDB files, specifically # T0467.t04.dssp-ebghstl.rdb (weight 1.53986) # T0467.t04.stride-ebghtl.rdb (weight 1.24869) # T0467.t04.str2.rdb (weight 1.54758) # T0467.t04.alpha.rdb (weight 0.659012) # T0467.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0467.t2k.stride-ebghtl.rdb (weight 1.24869) # T0467.t2k.str2.rdb (weight 1.54758) # T0467.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 T0467.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.stride-ebghtl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ # Comments from T0467.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ # Comments from T0467.t2k.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ # Comments from T0467.t2k.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1170 0.0733 0.8097 2 D 0.2434 0.0875 0.6691 3 L 0.3529 0.1142 0.5328 4 N 0.4008 0.1124 0.4868 5 R 0.3965 0.1034 0.5001 6 M 0.3215 0.0934 0.5852 7 G 0.2036 0.0756 0.7208 8 K 0.1660 0.0653 0.7688 9 D 0.3072 0.0419 0.6508 10 E 0.5597 0.0251 0.4151 11 Y 0.6530 0.0141 0.3329 12 Y 0.7790 0.0100 0.2110 13 V 0.8675 0.0066 0.1260 14 Q 0.8944 0.0054 0.1002 15 I 0.8817 0.0050 0.1133 16 T 0.7315 0.0161 0.2524 17 V 0.4395 0.0489 0.5116 18 D 0.3397 0.0321 0.6282 19 G 0.6412 0.0147 0.3441 20 K 0.8253 0.0062 0.1684 21 E 0.8985 0.0039 0.0976 22 V 0.8841 0.0052 0.1107 23 H 0.8547 0.0063 0.1390 24 S 0.6315 0.0180 0.3504 25 K 0.3520 0.0372 0.6109 26 A 0.1773 0.0731 0.7497 27 D 0.1246 0.0772 0.7982 28 N 0.1063 0.0818 0.8119 29 G 0.1507 0.0759 0.7733 30 Q 0.3017 0.0553 0.6430 31 K 0.3984 0.0467 0.5550 32 Y 0.5204 0.0422 0.4373 33 K 0.6465 0.0307 0.3228 34 D 0.7758 0.0127 0.2115 35 Y 0.8626 0.0062 0.1312 36 E 0.9049 0.0037 0.0915 37 Y 0.9066 0.0038 0.0896 38 K 0.9040 0.0038 0.0922 39 L 0.8444 0.0056 0.1500 40 T 0.8104 0.0119 0.1777 41 G 0.7340 0.0142 0.2518 42 F 0.7876 0.0094 0.2030 43 D 0.3413 0.0147 0.6441 44 K 0.0283 0.1242 0.8474 45 D 0.0495 0.0217 0.9287 46 G 0.0600 0.0275 0.9125 47 K 0.2887 0.0100 0.7013 48 E 0.8547 0.0033 0.1420 49 K 0.8678 0.0086 0.1237 50 E 0.9173 0.0034 0.0793 51 L 0.9089 0.0035 0.0876 52 E 0.9085 0.0039 0.0875 53 F 0.8855 0.0052 0.1094 54 T 0.7193 0.0194 0.2613 55 A 0.3734 0.0367 0.5899 56 Q 0.1280 0.0803 0.7917 57 K 0.1070 0.0878 0.8051 58 N 0.1434 0.1076 0.7491 59 L 0.1881 0.1040 0.7079 60 R 0.1314 0.0816 0.7869 61 K 0.0736 0.1700 0.7564 62 E 0.0920 0.0980 0.8101 63 A 0.4555 0.0361 0.5084 64 F 0.8438 0.0097 0.1465 65 L 0.9013 0.0061 0.0925 66 R 0.9202 0.0046 0.0752 67 V 0.9161 0.0047 0.0791 68 Y 0.9054 0.0054 0.0891 69 H 0.8368 0.0127 0.1505 70 S 0.3617 0.0483 0.5900 71 D 0.0887 0.0689 0.8425 72 K 0.1679 0.0654 0.7666 73 K 0.3241 0.0484 0.6275 74 G 0.4630 0.0282 0.5088 75 V 0.7259 0.0086 0.2656 76 S 0.7686 0.0215 0.2098 77 A 0.6893 0.0131 0.2976 78 W 0.3182 0.3465 0.3353 79 E 0.3186 0.3464 0.3350 80 E 0.3562 0.3006 0.3432 81 V 0.3150 0.0654 0.6196 82 K 0.2026 0.0600 0.7373 83 K 0.0230 0.7046 0.2724 84 D 0.0188 0.6699 0.3113 85 E 0.0317 0.5783 0.3899 86 L 0.0948 0.2737 0.6314 87 P 0.0484 0.2901 0.6615 88 A 0.0056 0.9225 0.0720 89 K 0.0050 0.9345 0.0605 90 V 0.0048 0.9462 0.0490 91 K 0.0052 0.9389 0.0559 92 E 0.0066 0.9006 0.0928 93 K 0.0093 0.8080 0.1827 94 L 0.0612 0.4733 0.4655 95 G 0.0940 0.1871 0.7190 96 V 0.1208 0.0596 0.8196 97 K 0.0488 0.0412 0.9100