# This file is the result of combining several RDB files, specifically # T0273.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0273.t2k.stride-ebghtl.rdb (weight 1.24869) # T0273.t2k.str2.rdb (weight 1.54758) # T0273.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 T0273.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0273 # 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 T0273.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 118 # # ============================================ # Comments from T0273.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0273 # 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 T0273.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 118 # # ============================================ # Comments from T0273.t2k.str2.rdb # ============================================ # TARGET T0273 # 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 T0273.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 118 # # ============================================ # Comments from T0273.t2k.alpha.rdb # ============================================ # TARGET T0273 # 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 T0273.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 118 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1117 0.0151 0.8732 2 P 0.3948 0.0180 0.5872 3 L 0.5708 0.0291 0.4002 4 V 0.5972 0.0281 0.3747 5 L 0.4171 0.0275 0.5554 6 D 0.1772 0.0385 0.7842 7 L 0.1412 0.0560 0.8027 8 A 0.2188 0.0828 0.6984 9 R 0.2397 0.0891 0.6712 10 P 0.3603 0.0623 0.5774 11 V 0.2619 0.0356 0.7025 12 S 0.1158 0.0252 0.8590 13 E 0.0058 0.9213 0.0730 14 E 0.0051 0.9327 0.0622 15 E 0.0057 0.9362 0.0580 16 L 0.0058 0.9300 0.0643 17 R 0.0104 0.8709 0.1187 18 R 0.0127 0.7005 0.2868 19 L 0.0387 0.4709 0.4904 20 S 0.0359 0.4142 0.5499 21 E 0.0236 0.3657 0.6107 22 L 0.0436 0.2549 0.7015 23 N 0.0772 0.0762 0.8466 24 P 0.0381 0.1781 0.7838 25 G 0.0835 0.1874 0.7290 26 Y 0.1821 0.3005 0.5174 27 Q 0.4314 0.2140 0.3546 28 W 0.6589 0.1179 0.2232 29 E 0.7512 0.0531 0.1958 30 R 0.6960 0.0633 0.2407 31 S 0.4745 0.0832 0.4423 32 P 0.0946 0.0279 0.8775 33 E 0.1257 0.0379 0.8364 34 G 0.7397 0.0087 0.2517 35 R 0.8891 0.0039 0.1071 36 L 0.8730 0.0064 0.1206 37 W 0.8297 0.0079 0.1624 38 V 0.5601 0.0131 0.4267 39 S 0.2816 0.0146 0.7038 40 P 0.1210 0.0298 0.8492 41 T 0.0906 0.0655 0.8439 42 G 0.0739 0.0790 0.8471 43 G 0.0678 0.1940 0.7382 44 E 0.0737 0.3724 0.5539 45 S 0.0633 0.5358 0.4009 46 G 0.0340 0.7340 0.2320 47 R 0.0198 0.8768 0.1033 48 R 0.0139 0.9237 0.0624 49 S 0.0073 0.9498 0.0429 50 L 0.0064 0.9546 0.0390 51 Q 0.0058 0.9573 0.0369 52 L 0.0049 0.9588 0.0363 53 A 0.0049 0.9584 0.0367 54 Y 0.0047 0.9558 0.0394 55 Q 0.0048 0.9512 0.0441 56 L 0.0049 0.9388 0.0563 57 A 0.0055 0.9214 0.0730 58 R 0.0069 0.8811 0.1121 59 W 0.0116 0.8318 0.1566 60 N 0.0321 0.7175 0.2504 61 E 0.0339 0.5815 0.3845 62 E 0.0338 0.4854 0.4807 63 R 0.0660 0.2368 0.6973 64 G 0.0744 0.1109 0.8147 65 L 0.2561 0.0627 0.6812 66 G 0.4786 0.0399 0.4814 67 V 0.7746 0.0240 0.2014 68 V 0.7911 0.0251 0.1839 69 F 0.7455 0.0266 0.2279 70 D 0.6108 0.0316 0.3576 71 S 0.3166 0.0432 0.6403 72 S 0.2042 0.1415 0.6543 73 T 0.2504 0.1230 0.6266 74 G 0.4053 0.0839 0.5108 75 F 0.5446 0.0481 0.4073 76 K 0.6286 0.0367 0.3347 77 F 0.3739 0.0334 0.5927 78 P 0.1117 0.0626 0.8258 79 D 0.0502 0.0727 0.8771 80 G 0.0541 0.0826 0.8633 81 S 0.1256 0.0773 0.7970 82 I 0.3206 0.0436 0.6358 83 L 0.4482 0.0384 0.5134 84 S 0.3208 0.0240 0.6551 85 P 0.2675 0.0217 0.7108 86 D 0.3289 0.0358 0.6354 87 A 0.7840 0.0311 0.1849 88 A 0.8936 0.0115 0.0949 89 F 0.9068 0.0094 0.0838 90 V 0.8499 0.0134 0.1367 91 E 0.5778 0.0261 0.3961 92 R 0.2829 0.1227 0.5944 93 G 0.1958 0.1519 0.6523 94 A 0.1885 0.1717 0.6398 95 W 0.0883 0.2078 0.7038 96 E 0.0581 0.2490 0.6929 97 A 0.0542 0.2744 0.6714 98 L 0.0621 0.2011 0.7368 99 S 0.0642 0.1808 0.7550 100 E 0.0309 0.5257 0.4435 101 A 0.0275 0.6623 0.3102 102 E 0.0331 0.6697 0.2972 103 R 0.0260 0.6811 0.2929 104 E 0.0268 0.5541 0.4191 105 G 0.0325 0.3547 0.6128 106 F 0.0602 0.2257 0.7141 107 P 0.0859 0.1559 0.7582 108 P 0.0698 0.1666 0.7636 109 L 0.1016 0.1026 0.7958 110 A 0.1269 0.0397 0.8334 111 P 0.1627 0.0433 0.7939 112 K 0.3138 0.0543 0.6320 113 A 0.7976 0.0127 0.1898 114 V 0.9082 0.0040 0.0878 115 F 0.9038 0.0048 0.0914 116 E 0.8991 0.0039 0.0970 117 V 0.8047 0.0054 0.1899 118 R 0.5895 0.0126 0.3979 119 S 0.2454 0.0121 0.7425 120 A 0.0169 0.1262 0.8570 121 S 0.0376 0.0573 0.9051 122 Q 0.0452 0.0552 0.8996 123 D 0.0675 0.0477 0.8848 124 P 0.0237 0.7143 0.2620 125 E 0.0091 0.8299 0.1610 126 E 0.0071 0.9036 0.0893 127 L 0.0051 0.9348 0.0601 128 R 0.0048 0.9460 0.0491 129 A 0.0047 0.9472 0.0480 130 K 0.0048 0.9496 0.0456 131 M 0.0047 0.9568 0.0384 132 G 0.0047 0.9588 0.0365 133 I 0.0047 0.9581 0.0372 134 Y 0.0048 0.9565 0.0387 135 L 0.0049 0.9445 0.0505 136 R 0.0062 0.8707 0.1231 137 N 0.0390 0.2717 0.6893 138 G 0.0386 0.0169 0.9446 139 V 0.0820 0.0097 0.9084 140 L 0.3857 0.0100 0.6044 141 L 0.8695 0.0052 0.1253 142 G 0.9058 0.0043 0.0899 143 V 0.9281 0.0033 0.0685 144 L 0.9173 0.0035 0.0792 145 V 0.8262 0.0063 0.1674 146 D 0.4418 0.0066 0.5517 147 P 0.0207 0.1393 0.8399 148 Y 0.0246 0.1344 0.8410 149 A 0.1319 0.0959 0.7722 150 R 0.3037 0.0314 0.6650 151 A 0.8720 0.0048 0.1232 152 V 0.9231 0.0037 0.0732 153 E 0.9286 0.0035 0.0679 154 V 0.9240 0.0035 0.0725 155 F 0.8866 0.0057 0.1076 156 R 0.5374 0.0103 0.4523 157 P 0.0641 0.0806 0.8554 158 G 0.0400 0.0621 0.8979 159 K 0.0906 0.0462 0.8632 160 P 0.1437 0.0454 0.8109 161 P 0.4082 0.0713 0.5205 162 L 0.6027 0.0718 0.3255 163 R 0.6886 0.0702 0.2412 164 L 0.5768 0.0894 0.3338 165 E 0.3803 0.1037 0.5160 166 G 0.2031 0.0779 0.7190 167 V 0.1307 0.1269 0.7424 168 E 0.1898 0.1274 0.6828 169 R 0.3098 0.0998 0.5904 170 V 0.3121 0.0649 0.6230 171 S 0.2410 0.0743 0.6846 172 L 0.1527 0.1539 0.6934 173 D 0.0779 0.2681 0.6539 174 P 0.1048 0.3579 0.5373 175 E 0.1626 0.2616 0.5759 176 L 0.1097 0.1128 0.7775 177 P 0.0346 0.1110 0.8545 178 G 0.0626 0.0596 0.8777 179 F 0.4707 0.0233 0.5060 180 A 0.7658 0.0106 0.2236 181 L 0.8092 0.0074 0.1835 182 S 0.6386 0.0149 0.3465 183 L 0.1471 0.5196 0.3332 184 P 0.0774 0.6286 0.2941 185 P 0.0806 0.5993 0.3201 186 L 0.0895 0.3482 0.5622 187 W 0.0358 0.0970 0.8672