# This file is the result of combining several RDB files, specifically # T0351.t04.dssp-ebghstl.rdb (weight 1.53986) # T0351.t04.stride-ebghtl.rdb (weight 1.24869) # T0351.t04.str2.rdb (weight 1.54758) # T0351.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 T0351.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0351 # Using neural net t06-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 T0351.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 5 # # ============================================ # Comments from T0351.t04.stride-ebghtl.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t04.str2.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t04.alpha.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0780 0.2765 0.6455 2 I 0.1400 0.4596 0.4004 3 L 0.0711 0.8161 0.1128 4 Y 0.0770 0.8318 0.0912 5 D 0.0887 0.8337 0.0776 6 A 0.1228 0.8011 0.0761 7 I 0.1024 0.8144 0.0832 8 M 0.1303 0.7699 0.0998 9 Y 0.1402 0.6847 0.1750 10 K 0.1266 0.5297 0.3437 11 Y 0.1063 0.1164 0.7772 12 P 0.0427 0.1692 0.7881 13 N 0.0673 0.1039 0.8287 14 A 0.1300 0.1155 0.7545 15 V 0.1733 0.0491 0.7776 16 S 0.2098 0.0642 0.7261 17 R 0.1872 0.1912 0.6216 18 K 0.2866 0.1487 0.5647 19 D 0.4799 0.0925 0.4276 20 F 0.6885 0.0224 0.2891 21 E 0.8477 0.0104 0.1419 22 L 0.8656 0.0114 0.1230 23 R 0.7082 0.0187 0.2731 24 N 0.4683 0.0391 0.4926 25 D 0.1434 0.0406 0.8160 26 G 0.0903 0.0584 0.8513 27 N 0.1193 0.0393 0.8414 28 G 0.1879 0.0474 0.7647 29 S 0.4019 0.0565 0.5416 30 Y 0.7769 0.0298 0.1933 31 I 0.7860 0.0351 0.1789 32 E 0.7720 0.0413 0.1867 33 K 0.8201 0.0346 0.1453 34 W 0.7351 0.0394 0.2256 35 N 0.6461 0.0243 0.3296 36 L 0.4334 0.0221 0.5445 37 R 0.1990 0.0431 0.7579 38 A 0.0971 0.0174 0.8854 39 P 0.0798 0.0317 0.8885 40 L 0.0853 0.0116 0.9031 41 P 0.0878 0.0136 0.8986 42 T 0.0656 0.0341 0.9002 43 Q 0.0048 0.9368 0.0584 44 A 0.0047 0.9562 0.0391 45 E 0.0047 0.9557 0.0396 46 L 0.0047 0.9553 0.0401 47 E 0.0047 0.9581 0.0373 48 T 0.0047 0.9534 0.0419 49 W 0.0047 0.9526 0.0426 50 W 0.0047 0.9568 0.0385 51 E 0.0047 0.9570 0.0383 52 E 0.0050 0.9492 0.0458 53 L 0.0062 0.9192 0.0747 54 Q 0.0113 0.8286 0.1601 55 K 0.0172 0.5889 0.3939 56 N 0.0545 0.0705 0.8750 57 P 0.0495 0.0373 0.9131 58 P 0.0299 0.1372 0.8329 59 Y 0.0461 0.1379 0.8160 60 E 0.0618 0.0386 0.8996 61 P 0.0564 0.0200 0.9236 62 P 0.0337 0.6166 0.3497 63 D 0.0371 0.7277 0.2351 64 Q 0.0211 0.8696 0.1093 65 V 0.0193 0.8907 0.0900 66 E 0.0269 0.8655 0.1076 67 L 0.0208 0.8510 0.1283 68 L 0.0204 0.7993 0.1803 69 A 0.0098 0.8423 0.1479 70 Q 0.0090 0.8354 0.1556 71 E 0.0103 0.8187 0.1710 72 L 0.0195 0.7343 0.2462 73 S 0.0186 0.6453 0.3361 74 Q 0.0092 0.8200 0.1709 75 E 0.0092 0.8902 0.1006 76 K 0.0058 0.9291 0.0650 77 L 0.0059 0.9318 0.0623 78 A 0.0054 0.9329 0.0617 79 R 0.0056 0.9380 0.0564 80 K 0.0051 0.9465 0.0484 81 Q 0.0048 0.9454 0.0498 82 L 0.0048 0.9436 0.0516 83 E 0.0048 0.9459 0.0493 84 E 0.0048 0.9390 0.0562 85 L 0.0051 0.9216 0.0734 86 N 0.0070 0.8916 0.1014 87 K 0.0062 0.8804 0.1134 88 T 0.0096 0.8727 0.1177 89 L 0.0282 0.7887 0.1832 90 G 0.0158 0.7787 0.2055 91 N 0.0105 0.8334 0.1561 92 E 0.0115 0.8699 0.1187 93 L 0.0158 0.8547 0.1295 94 S 0.0164 0.8044 0.1792 95 D 0.0219 0.7536 0.2245 96 I 0.1052 0.6800 0.2148 97 K 0.1735 0.5915 0.2350 98 L 0.2883 0.4732 0.2385 99 S 0.2665 0.4914 0.2421 100 L 0.3614 0.4615 0.1771 101 L 0.4360 0.3581 0.2059 102 S 0.4283 0.3193 0.2524 103 L 0.3786 0.3078 0.3135 104 K 0.2209 0.2290 0.5501 105 G 0.1331 0.1396 0.7273 106 D 0.1583 0.1440 0.6978 107 Y 0.0820 0.5239 0.3941 108 A 0.0567 0.5581 0.3852 109 E 0.0673 0.5732 0.3595 110 L 0.0877 0.5524 0.3599 111 E 0.1108 0.4981 0.3911 112 H 0.1126 0.4704 0.4170 113 H 0.1042 0.3408 0.5551 114 H 0.0890 0.2130 0.6981 115 H 0.0709 0.1659 0.7632 116 H 0.0745 0.1169 0.8086 117 H 0.0583 0.0511 0.8906