# This file is the result of combining several RDB files, specifically # T0407.t06.str2.rdb (weight 1.54425) # T0407.t06.str4.rdb (weight 0.924988) # T0407.t06.pb.rdb (weight 0.789901) # T0407.t06.bys.rdb (weight 0.748322) # T0407.t06.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 T0407.t06.str2.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-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 T0407.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 2 # # ============================================ # Comments from T0407.t06.str4.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.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 2 # # ============================================ # Comments from T0407.t06.pb.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.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 2 # # ============================================ # Comments from T0407.t06.bys.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.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 2 # # ============================================ # Comments from T0407.t06.alpha.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-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 T0407.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.3004 0.3348 0.3648 2 A 0.3531 0.3640 0.2829 3 Y 0.4036 0.3450 0.2514 4 F 0.2960 0.4847 0.2193 5 H 0.2386 0.5413 0.2202 6 E 0.3412 0.4529 0.2059 7 L 0.3755 0.3983 0.2262 8 L 0.4015 0.2892 0.3093 9 I 0.3253 0.2089 0.4658 10 G 0.1995 0.1609 0.6397 11 R 0.0619 0.5534 0.3846 12 E 0.0319 0.7086 0.2596 13 D 0.0228 0.7648 0.2124 14 L 0.0349 0.7072 0.2579 15 L 0.0509 0.6520 0.2971 16 R 0.0777 0.5554 0.3669 17 P 0.0302 0.7234 0.2463 18 F 0.0317 0.7240 0.2444 19 F 0.0580 0.7039 0.2381 20 E 0.0692 0.6658 0.2651 21 K 0.1058 0.5133 0.3809 22 C 0.2629 0.2867 0.4504 23 V 0.4070 0.1262 0.4667 24 K 0.4863 0.0918 0.4219 25 I 0.3975 0.2017 0.4007 26 E 0.3701 0.2673 0.3626 27 E 0.5253 0.1738 0.3009 28 V 0.5302 0.1129 0.3569 29 S 0.4841 0.1034 0.4125 30 R 0.3573 0.1937 0.4490 31 N 0.2360 0.1809 0.5831 32 E 0.2168 0.2408 0.5424 33 Q 0.1966 0.1522 0.6512 34 G 0.2591 0.0713 0.6696 35 V 0.5213 0.0186 0.4600 36 T 0.6670 0.0152 0.3178 37 L 0.7349 0.0150 0.2501 38 S 0.7138 0.0215 0.2647 39 I 0.6281 0.0521 0.3198 40 T 0.4774 0.0978 0.4248 41 N 0.3259 0.0972 0.5769 42 V 0.1777 0.3306 0.4917 43 T 0.1259 0.5229 0.3512 44 D 0.1772 0.5206 0.3022 45 L 0.2670 0.5360 0.1970 46 V 0.3004 0.5244 0.1752 47 L 0.3247 0.4778 0.1975 48 K 0.3422 0.4285 0.2293 49 L 0.2923 0.3915 0.3162 50 K 0.2505 0.3742 0.3753 51 K 0.2008 0.3997 0.3996 52 T 0.1779 0.3655 0.4566 53 A 0.1297 0.3708 0.4996 54 H 0.1427 0.2767 0.5806 55 D 0.1685 0.2218 0.6097 56 T 0.1473 0.3488 0.5039 57 L 0.3035 0.3289 0.3675 58 L 0.5335 0.2396 0.2269 59 V 0.6148 0.1917 0.1935 60 Y 0.6356 0.1510 0.2134 61 F 0.5588 0.1904 0.2509 62 R 0.3833 0.2845 0.3322 63 D 0.3086 0.2498 0.4415 64 M 0.3503 0.1802 0.4695 65 T 0.4000 0.0981 0.5019 66 L 0.3843 0.0633 0.5523 67 K 0.2706 0.0407 0.6887 68 P 0.2189 0.1462 0.6349 69 H 0.2063 0.1400 0.6537 70 T 0.3475 0.0983 0.5543 71 R 0.4825 0.0671 0.4505 72 Y 0.6656 0.0358 0.2985 73 T 0.7455 0.0139 0.2406 74 V 0.7968 0.0096 0.1936 75 R 0.7762 0.0114 0.2124 76 I 0.7655 0.0180 0.2165 77 G 0.6777 0.0403 0.2819 78 F 0.5044 0.1152 0.3804 79 K 0.2935 0.2325 0.4739 80 Q 0.1690 0.2073 0.6236 81 G 0.1670 0.1358 0.6972 82 I 0.3336 0.0670 0.5994 83 K 0.2979 0.0955 0.6066 84 G 0.2194 0.0820 0.6986 85 G 0.2135 0.1133 0.6732 86 D 0.3356 0.1021 0.5623 87 V 0.4637 0.0843 0.4520 88 N 0.4663 0.0802 0.4536 89 F 0.5964 0.0485 0.3552 90 E 0.6682 0.0395 0.2923 91 V 0.6706 0.0341 0.2953 92 T 0.5324 0.0848 0.3828 93 N 0.5875 0.0437 0.3689 94 F 0.7151 0.0253 0.2596 95 I 0.7356 0.0216 0.2428 96 V 0.7006 0.0203 0.2791 97 A 0.5120 0.0223 0.4657 98 P 0.2696 0.1187 0.6117 99 D 0.1817 0.1665 0.6518 100 K 0.0964 0.2656 0.6379 101 G 0.1005 0.1756 0.7239 102 L 0.3706 0.0659 0.5635 103 K 0.5504 0.0521 0.3975 104 Y 0.7367 0.0231 0.2402 105 T 0.7489 0.0170 0.2341 106 I 0.7693 0.0143 0.2164 107 S 0.6568 0.0200 0.3232 108 L 0.4303 0.0659 0.5038