# This file is the result of combining several RDB files, specifically # T0415.t04.str2.rdb (weight 1.54425) # T0415.t04.str4.rdb (weight 0.924988) # T0415.t04.pb.rdb (weight 0.789901) # T0415.t04.bys.rdb (weight 0.748322) # T0415.t04.alpha.rdb (weight 0.678173) # 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 T0415.t04.str2.rdb # ============================================ # TARGET T0415 # Using neural net dunbrack-40pc-3157-t04-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 T0415.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 1090 # # ============================================ # Comments from T0415.t04.str4.rdb # ============================================ # TARGET T0415 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0415.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 1090 # # ============================================ # Comments from T0415.t04.pb.rdb # ============================================ # TARGET T0415 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0415.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 1090 # # ============================================ # Comments from T0415.t04.bys.rdb # ============================================ # TARGET T0415 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0415.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 1090 # # ============================================ # Comments from T0415.t04.alpha.rdb # ============================================ # TARGET T0415 # Using neural net dunbrack-40pc-3157-t04-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 T0415.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 1090 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1471 0.0716 0.7814 2 K 0.2715 0.0483 0.6803 3 S 0.4295 0.0460 0.5245 4 V 0.6839 0.0132 0.3028 5 V 0.7502 0.0093 0.2405 6 T 0.7759 0.0054 0.2186 7 L 0.7752 0.0075 0.2172 8 K 0.7169 0.0124 0.2707 9 T 0.5057 0.0290 0.4653 10 T 0.2560 0.1141 0.6299 11 D 0.1606 0.1068 0.7327 12 G 0.2521 0.0659 0.6821 13 W 0.5154 0.0283 0.4563 14 I 0.6644 0.0166 0.3190 15 P 0.6637 0.0127 0.3236 16 V 0.6222 0.0169 0.3610 17 P 0.3185 0.0145 0.6670 18 F 0.1351 0.4282 0.4367 19 S 0.1375 0.4598 0.4027 20 K 0.3262 0.2676 0.4063 21 V 0.6402 0.0578 0.3020 22 M 0.7256 0.0457 0.2287 23 Y 0.8136 0.0118 0.1747 24 L 0.7964 0.0153 0.1883 25 E 0.7660 0.0190 0.2150 26 A 0.6748 0.0372 0.2879 27 K 0.4053 0.1091 0.4856 28 D 0.2107 0.0798 0.7095 29 K 0.2945 0.0560 0.6495 30 K 0.6294 0.0124 0.3582 31 T 0.7573 0.0070 0.2356 32 Y 0.8145 0.0050 0.1805 33 V 0.8263 0.0044 0.1694 34 N 0.7848 0.0081 0.2071 35 A 0.6834 0.0168 0.2998 36 E 0.4617 0.1260 0.4123 37 E 0.2752 0.1321 0.5927 38 L 0.2953 0.1254 0.5793 39 T 0.4445 0.0936 0.4619 40 G 0.5437 0.0943 0.3620 41 T 0.6195 0.0931 0.2874 42 H 0.6118 0.1033 0.2849 43 K 0.5121 0.1474 0.3405 44 Y 0.4206 0.1511 0.4283 45 S 0.3040 0.1116 0.5844 46 L 0.0373 0.7051 0.2576 47 Q 0.0112 0.8488 0.1399 48 E 0.0117 0.9048 0.0835 49 F 0.0108 0.9000 0.0892 50 E 0.0116 0.8775 0.1109 51 Y 0.0224 0.7892 0.1885 52 L 0.0639 0.5054 0.4307 53 L 0.1706 0.1257 0.7037 54 P 0.1313 0.1257 0.7430 55 K 0.0342 0.4227 0.5431 56 D 0.0509 0.3689 0.5802 57 S 0.1264 0.3534 0.5203 58 F 0.3119 0.2377 0.4504 59 I 0.4920 0.1826 0.3255 60 R 0.5582 0.1724 0.2694 61 C 0.5056 0.2016 0.2928 62 H 0.4358 0.2017 0.3625 63 R 0.3007 0.3440 0.3554 64 S 0.3128 0.3465 0.3406 65 F 0.4722 0.2623 0.2655 66 I 0.5475 0.2115 0.2410 67 V 0.5389 0.1805 0.2806 68 N 0.3868 0.1578 0.4554 69 V 0.0612 0.5919 0.3469 70 N 0.0581 0.6711 0.2709 71 H 0.1109 0.6387 0.2504 72 I 0.1529 0.5980 0.2491 73 K 0.1666 0.5764 0.2570 74 A 0.4023 0.3350 0.2628 75 I 0.4001 0.1847 0.4152 76 Y 0.3641 0.0450 0.5909 77 P 0.2250 0.1900 0.5850 78 D 0.1302 0.2040 0.6658 79 T 0.1275 0.1746 0.6979 80 H 0.1453 0.1177 0.7369 81 S 0.2632 0.0763 0.6605 82 T 0.6152 0.0210 0.3638 83 F 0.7718 0.0070 0.2212 84 L 0.8212 0.0044 0.1745 85 L 0.8279 0.0044 0.1677 86 S 0.8168 0.0045 0.1787 87 M 0.7624 0.0081 0.2295 88 D 0.5681 0.0427 0.3892 89 N 0.2051 0.0475 0.7474 90 G 0.1246 0.0723 0.8031 91 E 0.5253 0.0292 0.4455 92 R 0.6403 0.0258 0.3339 93 V 0.6669 0.0159 0.3172 94 P 0.5844 0.0236 0.3920 95 V 0.4860 0.0854 0.4286 96 S 0.2644 0.1490 0.5866 97 Q 0.0432 0.6776 0.2793 98 S 0.0196 0.7918 0.1886 99 Y 0.0243 0.8269 0.1488 100 A 0.0102 0.8953 0.0945 101 S 0.0085 0.9094 0.0820 102 Y 0.0084 0.9171 0.0744 103 F 0.0086 0.9117 0.0797 104 R 0.0086 0.9135 0.0778 105 K 0.0089 0.8958 0.0953 106 L 0.0144 0.7895 0.1960 107 L 0.0625 0.4057 0.5317 108 G 0.0444 0.1554 0.8003 109 F 0.1459 0.1018 0.7523