# This file is the result of combining several RDB files, specifically # T0327.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0327.t2k.stride-ebghtl.rdb (weight 1.24869) # T0327.t2k.str2.rdb (weight 1.54758) # T0327.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 T0327.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 7 # # ============================================ # Comments from T0327.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 7 # # ============================================ # Comments from T0327.t2k.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 7 # # ============================================ # Comments from T0327.t2k.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 7 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0334 0.1989 0.7677 2 N 0.0507 0.5389 0.4104 3 K 0.0164 0.7821 0.2015 4 D 0.0117 0.8497 0.1386 5 K 0.0144 0.8732 0.1125 6 L 0.0250 0.8820 0.0930 7 R 0.0298 0.8877 0.0825 8 Y 0.0468 0.8762 0.0770 9 A 0.0578 0.8498 0.0924 10 I 0.0725 0.8057 0.1217 11 L 0.0582 0.7430 0.1988 12 K 0.0561 0.4886 0.4554 13 E 0.0672 0.2563 0.6765 14 I 0.1230 0.2327 0.6443 15 F 0.1557 0.1984 0.6459 16 E 0.0870 0.1710 0.7419 17 G 0.0844 0.0908 0.8248 18 N 0.0819 0.1111 0.8071 19 T 0.1578 0.0860 0.7561 20 P 0.1952 0.0966 0.7082 21 L 0.2181 0.0633 0.7187 22 S 0.1506 0.0520 0.7974 23 E 0.0272 0.5361 0.4367 24 N 0.0222 0.5093 0.4685 25 D 0.0557 0.5184 0.4258 26 I 0.2586 0.1589 0.5825 27 G 0.4114 0.0633 0.5253 28 V 0.5190 0.0406 0.4404 29 T 0.2373 0.0474 0.7152 30 E 0.0142 0.8270 0.1588 31 D 0.0061 0.8858 0.1081 32 Q 0.0078 0.9020 0.0902 33 F 0.0049 0.9480 0.0471 34 D 0.0048 0.9550 0.0402 35 D 0.0047 0.9572 0.0380 36 A 0.0047 0.9590 0.0363 37 V 0.0047 0.9581 0.0372 38 N 0.0047 0.9565 0.0387 39 F 0.0049 0.9518 0.0434 40 L 0.0056 0.9461 0.0483 41 K 0.0067 0.9187 0.0746 42 R 0.0105 0.8223 0.1672 43 E 0.0443 0.1558 0.7999 44 G 0.0391 0.0366 0.9244 45 Y 0.3146 0.0560 0.6294 46 I 0.7744 0.0153 0.2103 47 I 0.7551 0.0352 0.2097 48 G 0.7529 0.0212 0.2259 49 V 0.7771 0.0180 0.2049 50 H 0.7714 0.0121 0.2165 51 Y 0.6223 0.0228 0.3550 52 S 0.3521 0.0430 0.6049 53 D 0.1326 0.0543 0.8131 54 D 0.0800 0.0675 0.8526 55 R 0.2140 0.0400 0.7460 56 P 0.4379 0.0522 0.5099 57 H 0.6136 0.0608 0.3255 58 L 0.6144 0.0843 0.3013 59 Y 0.4869 0.0912 0.4219 60 K 0.3104 0.1139 0.5757 61 L 0.1792 0.1054 0.7154 62 G 0.1853 0.0696 0.7451 63 P 0.2773 0.1405 0.5821 64 E 0.4952 0.1508 0.3539 65 L 0.5839 0.1227 0.2933 66 T 0.3998 0.1577 0.4425 67 E 0.1035 0.5746 0.3218 68 K 0.0402 0.5979 0.3619 69 G 0.0313 0.6926 0.2761 70 E 0.0220 0.8675 0.1105 71 N 0.0242 0.8932 0.0826 72 Y 0.0184 0.8912 0.0904 73 L 0.0212 0.8763 0.1024 74 K 0.0195 0.8206 0.1599 75 E 0.0177 0.7380 0.2443 76 N 0.0431 0.6535 0.3034 77 G 0.0167 0.6990 0.2843 78 T 0.0099 0.8081 0.1820 79 W 0.0071 0.9203 0.0726 80 S 0.0065 0.9381 0.0554 81 K 0.0063 0.9416 0.0521 82 A 0.0055 0.9454 0.0491 83 Y 0.0060 0.9463 0.0476 84 K 0.0062 0.9438 0.0501 85 T 0.0062 0.9366 0.0571 86 I 0.0069 0.9414 0.0517 87 K 0.0073 0.9352 0.0575 88 E 0.0090 0.9172 0.0738 89 I 0.0097 0.9027 0.0876 90 K 0.0108 0.8807 0.1085 91 D 0.0170 0.7900 0.1930 92 W 0.0267 0.6823 0.2910 93 I 0.0793 0.3310 0.5896 94 K 0.1015 0.2005 0.6980 95 L 0.0697 0.4612 0.4691 96 E 0.0616 0.4321 0.5063 97 H 0.0725 0.4090 0.5185 98 H 0.0912 0.3080 0.6008 99 H 0.1114 0.2558 0.6328 100 H 0.1146 0.2458 0.6396 101 H 0.0984 0.2359 0.6657 102 H 0.0947 0.1803 0.7250 103 M 0.0817 0.1784 0.7398 104 N 0.0839 0.1490 0.7671 105 K 0.0210 0.6719 0.3071 106 D 0.0339 0.7276 0.2384 107 K 0.0297 0.8580 0.1123 108 L 0.0582 0.8662 0.0756 109 R 0.0466 0.8911 0.0623 110 Y 0.0857 0.8613 0.0531 111 A 0.0944 0.8525 0.0531 112 I 0.0694 0.8693 0.0613 113 L 0.0648 0.8587 0.0765 114 K 0.0459 0.8673 0.0868 115 E 0.0545 0.8348 0.1107 116 I 0.0418 0.8253 0.1329 117 F 0.0491 0.7292 0.2218 118 E 0.0498 0.5241 0.4261 119 G 0.0494 0.2238 0.7268 120 N 0.0691 0.0944 0.8365 121 T 0.0833 0.0442 0.8724 122 P 0.0967 0.0713 0.8320 123 L 0.0961 0.1502 0.7537 124 S 0.1083 0.1324 0.7593 125 E 0.0553 0.3919 0.5529 126 N 0.0524 0.3342 0.6133 127 D 0.1015 0.2721 0.6264 128 I 0.1217 0.2173 0.6610 129 G 0.1404 0.1202 0.7394 130 V 0.2034 0.1111 0.6855 131 T 0.1710 0.1026 0.7264 132 E 0.0321 0.7668 0.2012 133 D 0.0198 0.7497 0.2305 134 Q 0.0236 0.7930 0.1834 135 F 0.0141 0.8556 0.1303 136 D 0.0146 0.8576 0.1278 137 D 0.0102 0.8962 0.0936 138 A 0.0080 0.9222 0.0697 139 V 0.0126 0.9177 0.0696 140 N 0.0114 0.8876 0.1009 141 F 0.0120 0.8545 0.1335 142 L 0.0311 0.8168 0.1522 143 K 0.0446 0.7342 0.2212 144 R 0.0863 0.5429 0.3708 145 E 0.0940 0.2285 0.6775 146 G 0.1362 0.0781 0.7857 147 Y 0.5740 0.0331 0.3930 148 I 0.8445 0.0191 0.1364 149 I 0.8362 0.0258 0.1380 150 G 0.7975 0.0142 0.1882 151 V 0.7130 0.0159 0.2711 152 H 0.5692 0.0187 0.4121 153 Y 0.3233 0.0461 0.6306 154 S 0.1448 0.0747 0.7805 155 D 0.0510 0.1185 0.8305 156 D 0.0505 0.0925 0.8569 157 R 0.0931 0.0820 0.8249 158 P 0.1297 0.1653 0.7050 159 H 0.2167 0.2841 0.4992 160 L 0.1969 0.4496 0.3535 161 Y 0.2418 0.4073 0.3509 162 K 0.2653 0.3319 0.4027 163 L 0.1743 0.2382 0.5875 164 G 0.0897 0.0944 0.8158 165 P 0.0562 0.3419 0.6019 166 E 0.0855 0.4133 0.5011 167 L 0.1583 0.3993 0.4424 168 T 0.1374 0.3585 0.5040 169 E 0.1060 0.4963 0.3977 170 K 0.0643 0.5460 0.3897 171 G 0.0543 0.5275 0.4182 172 E 0.0620 0.6093 0.3287 173 N 0.1036 0.6671 0.2293 174 Y 0.0976 0.6928 0.2096 175 L 0.1278 0.6455 0.2267 176 K 0.1280 0.5332 0.3388 177 E 0.0913 0.3977 0.5110 178 N 0.0683 0.1911 0.7406 179 G 0.0620 0.0828 0.8553 180 T 0.1230 0.1427 0.7343 181 W 0.0591 0.7506 0.1903 182 S 0.0348 0.8009 0.1643 183 K 0.0201 0.8425 0.1374 184 A 0.0164 0.8623 0.1214 185 Y 0.0152 0.8876 0.0972 186 K 0.0181 0.8060 0.1759 187 T 0.0191 0.7660 0.2148 188 I 0.0068 0.9305 0.0628 189 K 0.0062 0.9354 0.0584 190 E 0.0072 0.9225 0.0703 191 I 0.0076 0.9337 0.0587 192 K 0.0055 0.9438 0.0506 193 D 0.0063 0.9381 0.0556 194 W 0.0081 0.9308 0.0610 195 I 0.0121 0.9195 0.0684 196 K 0.0225 0.8743 0.1032 197 L 0.0309 0.8067 0.1624 198 E 0.0438 0.6813 0.2749 199 H 0.0568 0.5175 0.4257 200 H 0.0636 0.3675 0.5689 201 H 0.0862 0.2594 0.6545 202 H 0.0946 0.1685 0.7369 203 H 0.0740 0.0972 0.8288 204 H 0.0450 0.0354 0.9196