# This file is the result of combining several RDB files, specifically # T0237.t04.dssp-ebghstl.rdb (weight 1.53986) # T0237.t04.stride-ebghtl.rdb (weight 1.24869) # T0237.t04.str2.rdb (weight 1.54758) # T0237.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 T0237.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0237 # 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 T0237.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 3.64161 # # ============================================ # Comments from T0237.t04.stride-ebghtl.rdb # ============================================ # TARGET T0237 # 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 T0237.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 3.64161 # # ============================================ # Comments from T0237.t04.str2.rdb # ============================================ # TARGET T0237 # 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 T0237.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 3.64161 # # ============================================ # Comments from T0237.t04.alpha.rdb # ============================================ # TARGET T0237 # 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 T0237.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 3.64161 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.1797 0.0539 0.7664 2 G 0.3352 0.0368 0.6280 3 L 0.6044 0.0216 0.3739 4 W 0.6822 0.0205 0.2973 5 V 0.6117 0.0371 0.3512 6 D 0.2643 0.0419 0.6939 7 G 0.1426 0.0480 0.8094 8 N 0.2156 0.0535 0.7309 9 C 0.2148 0.3346 0.4506 10 E 0.1790 0.3191 0.5019 11 E 0.2283 0.2838 0.4878 12 I 0.1853 0.0546 0.7601 13 P 0.1614 0.0708 0.7678 14 Y 0.3004 0.1321 0.5676 15 V 0.4218 0.1650 0.4132 16 K 0.5078 0.1485 0.3437 17 E 0.5882 0.1291 0.2828 18 V 0.4436 0.1113 0.4451 19 E 0.2668 0.0917 0.6415 20 A 0.0511 0.4219 0.5270 21 E 0.0413 0.4056 0.5531 22 D 0.0579 0.3943 0.5478 23 L 0.0367 0.7237 0.2396 24 R 0.0309 0.7651 0.2040 25 E 0.0601 0.7141 0.2258 26 C 0.1074 0.6192 0.2733 27 N 0.1134 0.5045 0.3821 28 R 0.3098 0.4192 0.2710 29 I 0.5447 0.2693 0.1860 30 V 0.6582 0.1631 0.1787 31 F 0.5424 0.1202 0.3374 32 G 0.2059 0.0966 0.6975 33 A 0.1444 0.0911 0.7645 34 S 0.1550 0.1303 0.7148 35 A 0.0954 0.3635 0.5411 36 S 0.0649 0.2983 0.6368 37 D 0.0805 0.2643 0.6552 38 Q 0.0716 0.1087 0.8197 39 P 0.0659 0.2303 0.7038 40 T 0.0805 0.3678 0.5517 41 Q 0.1375 0.4378 0.4247 42 Y 0.1172 0.5816 0.3012 43 E 0.0872 0.6135 0.2992 44 E 0.0597 0.6141 0.3263 45 E 0.0579 0.6130 0.3290 46 M 0.0409 0.7066 0.2525 47 T 0.0263 0.7260 0.2477 48 D 0.0271 0.7802 0.1927 49 Y 0.0075 0.9214 0.0711 50 Q 0.0053 0.9501 0.0445 51 K 0.0059 0.9527 0.0414 52 I 0.0057 0.9500 0.0443 53 Q 0.0057 0.9507 0.0436 54 Q 0.0064 0.9278 0.0658 55 G 0.0074 0.8818 0.1108 56 F 0.0193 0.8348 0.1459 57 R 0.0317 0.8250 0.1433 58 Q 0.0233 0.8152 0.1615 59 N 0.0234 0.7024 0.2743 60 N 0.0634 0.5685 0.3681 61 R 0.0058 0.9281 0.0661 62 E 0.0077 0.9331 0.0592 63 M 0.0116 0.9231 0.0653 64 I 0.0167 0.9076 0.0757 65 K 0.0202 0.8669 0.1129 66 S 0.0236 0.7445 0.2319 67 A 0.0498 0.6435 0.3067 68 F 0.1394 0.3473 0.5134 69 L 0.1686 0.0870 0.7444 70 P 0.2222 0.0913 0.6865 71 V 0.1915 0.2100 0.5985 72 G 0.1816 0.1771 0.6412 73 A 0.2425 0.1748 0.5827 74 F 0.3091 0.1396 0.5513 75 N 0.2431 0.0804 0.6765 76 S 0.1341 0.2094 0.6566 77 D 0.0971 0.2042 0.6986 78 N 0.1530 0.2103 0.6367 79 F 0.3109 0.1520 0.5371 80 K 0.3726 0.1334 0.4940 81 S 0.3185 0.1104 0.5711 82 K 0.1454 0.0838 0.7709 83 G 0.1163 0.0376 0.8461 84 R 0.2285 0.0668 0.7047 85 G 0.4138 0.0429 0.5433 86 F 0.4776 0.0403 0.4821 87 N 0.4552 0.0384 0.5064 88 W 0.3494 0.1444 0.5062 89 A 0.3782 0.1433 0.4785 90 N 0.4571 0.1124 0.4305 91 F 0.3792 0.1269 0.4939 92 D 0.2290 0.1123 0.6586 93 S 0.0623 0.2768 0.6608 94 V 0.0820 0.2773 0.6407 95 K 0.1188 0.1579 0.7233 96 K 0.1863 0.0993 0.7144 97 K 0.5541 0.0797 0.3663 98 C 0.7538 0.0410 0.2051 99 Y 0.7698 0.0595 0.1708 100 I 0.8081 0.0677 0.1242 101 F 0.7058 0.0824 0.2118 102 N 0.5148 0.0651 0.4200 103 T 0.3059 0.0416 0.6525 104 K 0.2200 0.0225 0.7575 105 P 0.2407 0.0515 0.7078 106 T 0.3713 0.1017 0.5270 107 C 0.5889 0.1032 0.3079 108 L 0.6609 0.0939 0.2453 109 I 0.5895 0.0916 0.3189 110 N 0.3550 0.0817 0.5633 111 D 0.1460 0.0758 0.7782 112 K 0.0375 0.2888 0.6738 113 N 0.0768 0.2218 0.7014 114 F 0.4272 0.2387 0.3341 115 I 0.6519 0.2085 0.1396 116 A 0.6249 0.2666 0.1085 117 T 0.5499 0.3322 0.1179 118 T 0.4163 0.4130 0.1707 119 A 0.3571 0.3888 0.2542 120 L 0.2938 0.2712 0.4350 121 S 0.1810 0.1800 0.6390 122 H 0.0868 0.0376 0.8756 123 P 0.0301 0.2336 0.7362 124 Q 0.0384 0.2406 0.7210 125 E 0.0643 0.2056 0.7301