# This file is the result of combining several RDB files, specifically # T0197.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0197.t2k.stride-ebghtl.rdb (weight 1.24869) # T0197.t2k.str2.rdb (weight 1.54758) # T0197.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 T0197.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0197 # 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 T0197.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 43 # # ============================================ # Comments from T0197.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0197 # 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 T0197.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 43 # # ============================================ # Comments from T0197.t2k.str2.rdb # ============================================ # TARGET T0197 # 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 T0197.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 43 # # ============================================ # Comments from T0197.t2k.alpha.rdb # ============================================ # TARGET T0197 # 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 T0197.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 43 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0694 0.1206 0.8101 2 H 0.1267 0.1718 0.7015 3 H 0.1538 0.2254 0.6208 4 H 0.1658 0.2445 0.5897 5 H 0.2387 0.1595 0.6018 6 H 0.2361 0.1069 0.6570 7 H 0.2739 0.0663 0.6598 8 G 0.5678 0.0358 0.3964 9 S 0.8240 0.0126 0.1634 10 E 0.8876 0.0076 0.1048 11 V 0.9017 0.0077 0.0906 12 E 0.9075 0.0055 0.0869 13 I 0.8863 0.0081 0.1056 14 K 0.8795 0.0075 0.1129 15 F 0.8460 0.0091 0.1449 16 K 0.7103 0.0165 0.2733 17 I 0.3720 0.0227 0.6053 18 K 0.1873 0.0164 0.7962 19 L 0.0101 0.8526 0.1373 20 E 0.0056 0.9255 0.0689 21 D 0.0055 0.9397 0.0548 22 F 0.0048 0.9531 0.0421 23 L 0.0049 0.9556 0.0395 24 H 0.0048 0.9556 0.0397 25 T 0.0048 0.9558 0.0394 26 L 0.0049 0.9492 0.0459 27 N 0.0052 0.9306 0.0642 28 T 0.0071 0.8518 0.1411 29 F 0.0314 0.6026 0.3660 30 N 0.0568 0.2002 0.7431 31 P 0.0387 0.3787 0.5825 32 E 0.0534 0.5046 0.4419 33 F 0.1041 0.4519 0.4440 34 V 0.1522 0.4294 0.4184 35 R 0.2113 0.4261 0.3626 36 Y 0.2940 0.4722 0.2338 37 E 0.2891 0.4641 0.2468 38 E 0.3379 0.3986 0.2635 39 Q 0.3275 0.3472 0.3253 40 E 0.3108 0.2804 0.4088 41 D 0.3214 0.1996 0.4790 42 V 0.3904 0.2084 0.4012 43 Y 0.4183 0.1844 0.3973 44 F 0.3470 0.1441 0.5089 45 E 0.2404 0.0849 0.6747 46 V 0.1055 0.0441 0.8504 47 P 0.0554 0.0975 0.8471 48 R 0.0529 0.1601 0.7870 49 P 0.0360 0.3441 0.6199 50 K 0.0501 0.4574 0.4925 51 L 0.0453 0.6683 0.2863 52 L 0.0574 0.7053 0.2372 53 R 0.1006 0.7011 0.1983 54 I 0.1449 0.6553 0.1998 55 R 0.1833 0.6221 0.1946 56 G 0.2031 0.6292 0.1677 57 V 0.2208 0.5834 0.1958 58 H 0.2192 0.4298 0.3510 59 N 0.1752 0.2083 0.6164 60 L 0.0813 0.1120 0.8067 61 K 0.0670 0.0812 0.8519 62 K 0.3109 0.0490 0.6401 63 Y 0.6780 0.0150 0.3070 64 Y 0.8137 0.0097 0.1766 65 L 0.8427 0.0108 0.1464 66 T 0.7827 0.0226 0.1947 67 F 0.7316 0.0253 0.2431 68 K 0.4604 0.0578 0.4818 69 E 0.2709 0.0394 0.6897 70 I 0.1958 0.0663 0.7379 71 L 0.1635 0.0908 0.7457 72 D 0.1072 0.1138 0.7791 73 E 0.0763 0.1058 0.8178 74 N 0.1025 0.0829 0.8146 75 N 0.1917 0.0913 0.7169 76 E 0.3300 0.1217 0.5482 77 E 0.4337 0.1244 0.4418 78 F 0.4891 0.1375 0.3734 79 Y 0.6242 0.1264 0.2494 80 E 0.7182 0.0881 0.1937 81 V 0.7320 0.0724 0.1956 82 E 0.7750 0.0309 0.1941 83 F 0.6613 0.0226 0.3162 84 E 0.5094 0.0147 0.4759 85 I 0.2558 0.0338 0.7103 86 G 0.0826 0.0460 0.8714 87 D 0.0897 0.0306 0.8797 88 F 0.0081 0.8424 0.1495 89 E 0.0058 0.9240 0.0702 90 K 0.0052 0.9435 0.0514 91 A 0.0048 0.9564 0.0388 92 V 0.0048 0.9583 0.0369 93 E 0.0047 0.9568 0.0384 94 V 0.0047 0.9575 0.0378 95 F 0.0048 0.9545 0.0407 96 K 0.0049 0.9417 0.0534 97 R 0.0055 0.8817 0.1127 98 L 0.0397 0.4493 0.5110 99 G 0.0352 0.0704 0.8944 100 F 0.0818 0.0621 0.8561 101 K 0.3187 0.0804 0.6009 102 I 0.5066 0.1005 0.3929 103 Q 0.5874 0.1194 0.2931 104 A 0.5733 0.1363 0.2904 105 T 0.6003 0.1548 0.2449 106 I 0.6648 0.1626 0.1726 107 K 0.7223 0.1278 0.1498 108 K 0.7673 0.0875 0.1452 109 K 0.7756 0.0831 0.1413 110 R 0.6975 0.1232 0.1794 111 W 0.7469 0.1051 0.1479 112 V 0.7594 0.0975 0.1431 113 Y 0.8105 0.0634 0.1262 114 K 0.7700 0.0578 0.1722 115 L 0.5229 0.0665 0.4106 116 N 0.0992 0.0492 0.8516 117 G 0.1391 0.0514 0.8095 118 V 0.8139 0.0054 0.1807 119 T 0.9120 0.0035 0.0845 120 L 0.9228 0.0036 0.0736 121 E 0.9091 0.0051 0.0858 122 V 0.8645 0.0089 0.1266 123 N 0.6267 0.0397 0.3336 124 R 0.2748 0.1288 0.5964 125 V 0.1614 0.1594 0.6792 126 E 0.0971 0.1564 0.7466 127 G 0.0900 0.1165 0.7934 128 I 0.1571 0.1320 0.7110 129 G 0.1652 0.1318 0.7030 130 D 0.1892 0.1516 0.6592 131 F 0.5844 0.0800 0.3356 132 V 0.7409 0.0384 0.2207 133 D 0.8700 0.0188 0.1112 134 I 0.8860 0.0196 0.0944 135 E 0.8629 0.0228 0.1143 136 V 0.8121 0.0309 0.1570 137 I 0.6677 0.0424 0.2899 138 S 0.3286 0.0574 0.6140 139 D 0.0966 0.0614 0.8420 140 S 0.0608 0.0489 0.8903 141 P 0.0214 0.3363 0.6423 142 E 0.0074 0.8360 0.1566 143 E 0.0064 0.8951 0.0984 144 A 0.0050 0.9384 0.0566 145 K 0.0048 0.9541 0.0412 146 E 0.0048 0.9570 0.0383 147 K 0.0047 0.9586 0.0367 148 I 0.0047 0.9583 0.0369 149 W 0.0047 0.9598 0.0355 150 E 0.0047 0.9605 0.0348 151 V 0.0047 0.9600 0.0352 152 A 0.0048 0.9574 0.0378 153 K 0.0055 0.9438 0.0508 154 M 0.0071 0.8913 0.1016 155 L 0.0450 0.5158 0.4393 156 G 0.0407 0.0328 0.9265 157 L 0.0627 0.0095 0.9278 158 K 0.0621 0.0108 0.9271 159 E 0.0100 0.7403 0.2496 160 E 0.0118 0.7666 0.2216 161 D 0.0205 0.7740 0.2055 162 V 0.0541 0.6981 0.2478 163 E 0.0969 0.6517 0.2514 164 P 0.0586 0.7859 0.1555 165 R 0.0360 0.8360 0.1279 166 L 0.0279 0.8599 0.1122 167 Y 0.0075 0.9456 0.0469 168 L 0.0074 0.9492 0.0434 169 E 0.0065 0.9493 0.0441 170 L 0.0061 0.9442 0.0497 171 I 0.0067 0.9196 0.0738 172 N 0.0077 0.8668 0.1255 173 E 0.0133 0.7374 0.2493 174 L 0.0256 0.5539 0.4205 175 S 0.0551 0.3315 0.6134 176 G 0.0539 0.1845 0.7616 177 R 0.0562 0.1605 0.7833 178 S 0.0470 0.0907 0.8623 179 S 0.0369 0.0481 0.9149