# This file is the result of combining several RDB files, specifically # T0209.t04.dssp-ebghstl.rdb (weight 1.53986) # T0209.t04.stride-ebghtl.rdb (weight 1.24869) # T0209.t04.str2.rdb (weight 1.54758) # T0209.t04.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 T0209.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 23.6728 # # ============================================ # Comments from T0209.t04.stride-ebghtl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 23.6728 # # ============================================ # Comments from T0209.t04.str2.rdb # ============================================ # TARGET T0209 # 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 T0209.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 23.6728 # # ============================================ # Comments from T0209.t04.alpha.rdb # ============================================ # TARGET T0209 # 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 T0209.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 23.6728 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1025 0.0378 0.8596 2 N 0.1222 0.0743 0.8034 3 D 0.2305 0.1136 0.6559 4 L 0.3979 0.0772 0.5249 5 T 0.5924 0.0301 0.3775 6 L 0.6404 0.0127 0.3469 7 S 0.4949 0.0146 0.4905 8 P 0.5306 0.0178 0.4515 9 I 0.7505 0.0189 0.2305 10 A 0.8825 0.0072 0.1102 11 I 0.9078 0.0058 0.0864 12 I 0.8898 0.0057 0.1044 13 H 0.6849 0.0267 0.2884 14 T 0.2951 0.0158 0.6891 15 P 0.1245 0.1128 0.7626 16 Y 0.1385 0.1488 0.7127 17 K 0.2038 0.1861 0.6101 18 E 0.2779 0.1704 0.5517 19 K 0.3392 0.1834 0.4774 20 F 0.2911 0.1003 0.6087 21 S 0.2231 0.0703 0.7066 22 V 0.1673 0.0251 0.8076 23 P 0.1406 0.0429 0.8165 24 R 0.1777 0.0493 0.7730 25 Q 0.1463 0.0385 0.8152 26 P 0.1018 0.1939 0.7043 27 N 0.1877 0.2410 0.5713 28 L 0.3302 0.1966 0.4732 29 V 0.3227 0.1182 0.5592 30 E 0.2296 0.1321 0.6383 31 D 0.1335 0.0708 0.7958 32 G 0.3118 0.0419 0.6463 33 V 0.7322 0.0147 0.2531 34 G 0.8798 0.0069 0.1133 35 I 0.9247 0.0045 0.0708 36 V 0.9262 0.0038 0.0700 37 E 0.9182 0.0044 0.0774 38 L 0.8303 0.0065 0.1632 39 L 0.3406 0.0158 0.6435 40 P 0.0922 0.0573 0.8505 41 P 0.0485 0.1689 0.7826 42 Y 0.0691 0.1355 0.7955 43 N 0.0703 0.0558 0.8739 44 S 0.0789 0.0413 0.8798 45 P 0.0083 0.7724 0.2193 46 E 0.0098 0.7907 0.1995 47 A 0.0100 0.8555 0.1345 48 V 0.0265 0.7891 0.1844 49 R 0.0255 0.6822 0.2922 50 G 0.0403 0.5056 0.4541 51 L 0.0449 0.5724 0.3828 52 E 0.0461 0.5509 0.4030 53 Q 0.0518 0.4028 0.5454 54 F 0.1212 0.1651 0.7136 55 S 0.1120 0.1277 0.7603 56 H 0.4652 0.0741 0.4608 57 L 0.8429 0.0117 0.1454 58 W 0.9206 0.0061 0.0734 59 L 0.9249 0.0049 0.0702 60 I 0.9185 0.0090 0.0726 61 F 0.8957 0.0136 0.0907 62 Q 0.8528 0.0222 0.1250 63 F 0.6677 0.0569 0.2754 64 D 0.4151 0.0811 0.5038 65 Q 0.2785 0.2078 0.5137 66 I 0.2042 0.2156 0.5803 67 Q 0.1156 0.2031 0.6813 68 Q 0.0598 0.1296 0.8106 69 G 0.0452 0.0779 0.8769 70 K 0.1132 0.0589 0.8280 71 W 0.2938 0.0260 0.6802 72 Q 0.3669 0.0187 0.6144 73 P 0.4386 0.0285 0.5329 74 T 0.6042 0.0283 0.3676 75 V 0.6363 0.0144 0.3493 76 R 0.4421 0.0128 0.5451 77 P 0.2623 0.0135 0.7242 78 P 0.2123 0.0645 0.7232 79 R 0.1924 0.0896 0.7180 80 L 0.1215 0.1034 0.7751 81 G 0.0734 0.0593 0.8673 82 G 0.0650 0.0522 0.8828 83 N 0.1408 0.0420 0.8172 84 Q 0.3181 0.0457 0.6362 85 R 0.6426 0.0241 0.3333 86 V 0.7940 0.0250 0.1809 87 G 0.8513 0.0123 0.1363 88 V 0.8827 0.0116 0.1056 89 F 0.8758 0.0135 0.1107 90 A 0.7667 0.0187 0.2146 91 S 0.5352 0.0311 0.4337 92 R 0.2539 0.0480 0.6982 93 A 0.1461 0.0501 0.8038 94 T 0.0816 0.1175 0.8009 95 H 0.1051 0.0882 0.8067 96 R 0.1092 0.0374 0.8534 97 P 0.0990 0.0517 0.8493 98 N 0.1288 0.0321 0.8391 99 P 0.1365 0.2315 0.6320 100 L 0.2406 0.2164 0.5430 101 G 0.5327 0.1135 0.3539 102 L 0.6475 0.0488 0.3037 103 S 0.6639 0.0384 0.2977 104 K 0.7969 0.0240 0.1791 105 V 0.8675 0.0074 0.1251 106 E 0.8981 0.0063 0.0956 107 L 0.8952 0.0074 0.0974 108 R 0.8174 0.0317 0.1509 109 Q 0.8706 0.0098 0.1196 110 V 0.8866 0.0064 0.1070 111 E 0.8946 0.0061 0.0993 112 C 0.8567 0.0082 0.1351 113 I 0.5758 0.0377 0.3865 114 N 0.1289 0.0312 0.8399 115 G 0.0547 0.0309 0.9144 116 N 0.2467 0.0259 0.7274 117 I 0.7863 0.0052 0.2085 118 F 0.9081 0.0037 0.0882 119 L 0.9228 0.0035 0.0737 120 H 0.9218 0.0035 0.0747 121 L 0.8489 0.0053 0.1458 122 G 0.5086 0.0350 0.4563 123 A 0.4668 0.0293 0.5040 124 V 0.5580 0.0395 0.4025 125 D 0.6385 0.0480 0.3135 126 L 0.4802 0.1590 0.3608 127 V 0.3868 0.1430 0.4702 128 D 0.1275 0.0771 0.7954 129 G 0.1006 0.0376 0.8618 130 T 0.2481 0.0153 0.7366 131 P 0.5401 0.0117 0.4483 132 I 0.7735 0.0219 0.2046 133 F 0.8167 0.0191 0.1642 134 D 0.7894 0.0160 0.1947 135 I 0.6481 0.0265 0.3254 136 K 0.4490 0.0467 0.5044 137 P 0.3638 0.0708 0.5654 138 Y 0.2295 0.0786 0.6920 139 I 0.1385 0.0305 0.8310 140 A 0.0607 0.0359 0.9034