# This file is the result of combining several RDB files, specifically # T0187.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0187.t2k.stride-ebghtl.rdb (weight 1.24869) # T0187.t2k.str.rdb (weight 1.53983) # T0187.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 T0187.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 30 # # ============================================ # Comments from T0187.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 30 # # ============================================ # Comments from T0187.t2k.str.rdb # ============================================ # TARGET T0187 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0187.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 30 # # ============================================ # Comments from T0187.t2k.alpha.rdb # ============================================ # TARGET T0187 # 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 T0187.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 30 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0452 0.0413 0.9135 2 F 0.0936 0.0717 0.8347 3 D 0.0668 0.0924 0.8408 4 P 0.0375 0.3105 0.6520 5 E 0.0148 0.5833 0.4020 6 S 0.0274 0.6217 0.3509 7 L 0.0075 0.8261 0.1663 8 K 0.0060 0.8844 0.1095 9 K 0.0052 0.9151 0.0796 10 L 0.0049 0.9341 0.0610 11 A 0.0047 0.9392 0.0561 12 I 0.0045 0.9507 0.0448 13 E 0.0046 0.9501 0.0453 14 I 0.0045 0.9546 0.0409 15 V 0.0044 0.9556 0.0400 16 K 0.0044 0.9551 0.0405 17 K 0.0046 0.9480 0.0475 18 S 0.0046 0.9393 0.0561 19 I 0.0049 0.9094 0.0857 20 E 0.0055 0.8363 0.1582 21 A 0.0110 0.6559 0.3331 22 V 0.0525 0.3041 0.6434 23 F 0.0886 0.0509 0.8605 24 P 0.0086 0.7043 0.2870 25 D 0.0061 0.8650 0.1290 26 R 0.0073 0.9112 0.0815 27 A 0.0132 0.9051 0.0817 28 V 0.0161 0.8779 0.1059 29 K 0.0167 0.8168 0.1665 30 E 0.0160 0.6396 0.3443 31 T 0.0324 0.4753 0.4923 32 L 0.1253 0.0920 0.7827 33 P 0.1295 0.0735 0.7971 34 K 0.1675 0.0864 0.7461 35 L 0.1010 0.0834 0.8156 36 N 0.0672 0.1376 0.7952 37 L 0.0599 0.0730 0.8672 38 D 0.0746 0.0671 0.8583 39 R 0.3428 0.0121 0.6451 40 V 0.7616 0.0040 0.2343 41 I 0.9153 0.0040 0.0807 42 L 0.9293 0.0037 0.0670 43 V 0.8884 0.0242 0.0875 44 A 0.8151 0.0173 0.1675 45 V 0.4194 0.0729 0.5077 46 G 0.1318 0.1876 0.6807 47 K 0.0261 0.6919 0.2820 48 A 0.0132 0.8058 0.1809 49 A 0.0052 0.8908 0.1039 50 W 0.0045 0.9414 0.0541 51 R 0.0044 0.9371 0.0585 52 M 0.0044 0.9492 0.0464 53 A 0.0044 0.9542 0.0415 54 K 0.0044 0.9563 0.0392 55 A 0.0044 0.9524 0.0433 56 A 0.0044 0.9555 0.0401 57 Y 0.0045 0.9518 0.0436 58 E 0.0050 0.9340 0.0610 59 V 0.0085 0.8637 0.1277 60 L 0.0380 0.6889 0.2730 61 G 0.0232 0.4729 0.5039 62 K 0.0344 0.3366 0.6290 63 K 0.0646 0.3390 0.5963 64 I 0.1726 0.2108 0.6166 65 R 0.1992 0.1125 0.6884 66 K 0.2076 0.0630 0.7294 67 G 0.5658 0.0169 0.4172 68 V 0.8796 0.0048 0.1157 69 V 0.9053 0.0041 0.0905 70 V 0.8887 0.0046 0.1067 71 T 0.7275 0.0073 0.2652 72 K 0.3720 0.0211 0.6069 73 Y 0.0611 0.0909 0.8481 74 G 0.0481 0.0780 0.8739 75 H 0.1065 0.0886 0.8049 76 S 0.1518 0.0671 0.7811 77 E 0.1695 0.0579 0.7726 78 G 0.1411 0.0678 0.7911 79 P 0.1630 0.0815 0.7555 80 I 0.1499 0.0515 0.7986 81 D 0.1188 0.0780 0.8032 82 D 0.3668 0.0458 0.5874 83 F 0.6740 0.0101 0.3159 84 E 0.8460 0.0075 0.1465 85 I 0.9000 0.0052 0.0948 86 Y 0.8465 0.0145 0.1390 87 E 0.7646 0.0112 0.2242 88 A 0.4527 0.0247 0.5226 89 G 0.1980 0.0361 0.7659 90 H 0.1047 0.0267 0.8686 91 P 0.1375 0.0421 0.8203 92 V 0.1468 0.0276 0.8256 93 P 0.0936 0.0400 0.8664 94 D 0.0650 0.1017 0.8333 95 E 0.0083 0.7577 0.2339 96 N 0.0085 0.8150 0.1765 97 T 0.0061 0.9243 0.0696 98 I 0.0044 0.9553 0.0403 99 K 0.0044 0.9578 0.0378 100 T 0.0044 0.9561 0.0395 101 T 0.0044 0.9590 0.0366 102 R 0.0044 0.9598 0.0358 103 R 0.0044 0.9586 0.0370 104 V 0.0044 0.9575 0.0381 105 L 0.0045 0.9548 0.0407 106 E 0.0045 0.9487 0.0467 107 L 0.0054 0.9146 0.0800 108 V 0.0135 0.8620 0.1245 109 D 0.0086 0.6682 0.3233 110 Q 0.0142 0.2784 0.7074 111 L 0.0572 0.0629 0.8799 112 N 0.0506 0.0236 0.9259 113 E 0.0119 0.2638 0.7243 114 N 0.0206 0.1569 0.8225 115 D 0.1864 0.0992 0.7144 116 T 0.7896 0.0088 0.2016 117 V 0.9243 0.0038 0.0719 118 L 0.9319 0.0036 0.0645 119 F 0.9297 0.0036 0.0667 120 L 0.8874 0.0054 0.1072 121 L 0.7096 0.0163 0.2741 122 S 0.4045 0.0262 0.5693 123 G 0.1234 0.0811 0.7954 124 G 0.0662 0.1997 0.7341 125 G 0.0690 0.4162 0.5147 126 S 0.0901 0.4943 0.4156 127 S 0.1117 0.4788 0.4095 128 L 0.1866 0.3372 0.4762 129 F 0.2217 0.1710 0.6073 130 E 0.3303 0.0819 0.5878 131 L 0.2591 0.0513 0.6895 132 P 0.1755 0.0619 0.7626 133 L 0.0633 0.2597 0.6771 134 E 0.0277 0.1583 0.8140 135 G 0.0429 0.0847 0.8724 136 V 0.2005 0.0118 0.7878 137 S 0.1173 0.0126 0.8701 138 L 0.0056 0.8989 0.0954 139 E 0.0045 0.9361 0.0594 140 E 0.0048 0.9453 0.0499 141 I 0.0045 0.9503 0.0453 142 Q 0.0045 0.9467 0.0489 143 K 0.0046 0.9381 0.0573 144 L 0.0046 0.9271 0.0683 145 T 0.0052 0.9226 0.0722 146 S 0.0050 0.9146 0.0804 147 A 0.0053 0.8757 0.1189 148 L 0.0071 0.7887 0.2042 149 L 0.0224 0.5341 0.4435 150 K 0.0210 0.1196 0.8594