# This file is the result of combining several RDB files, specifically # T0367.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0367.t2k.stride-ebghtl.rdb (weight 1.24869) # T0367.t2k.str2.rdb (weight 1.54758) # T0367.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 T0367.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0367 # 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 T0367.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 38 # # ============================================ # Comments from T0367.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0367 # 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 T0367.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 38 # # ============================================ # Comments from T0367.t2k.str2.rdb # ============================================ # TARGET T0367 # 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 T0367.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 38 # # ============================================ # Comments from T0367.t2k.alpha.rdb # ============================================ # TARGET T0367 # 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 T0367.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 38 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0348 0.1695 0.7957 2 D 0.0302 0.5165 0.4533 3 E 0.0072 0.8332 0.1595 4 L 0.0048 0.9226 0.0725 5 E 0.0050 0.9417 0.0532 6 L 0.0050 0.9453 0.0497 7 R 0.0050 0.9451 0.0499 8 I 0.0050 0.9521 0.0429 9 R 0.0052 0.9463 0.0485 10 K 0.0050 0.9415 0.0535 11 A 0.0049 0.9430 0.0521 12 E 0.0050 0.9463 0.0487 13 K 0.0051 0.9382 0.0567 14 L 0.0058 0.9289 0.0653 15 V 0.0051 0.9442 0.0508 16 Q 0.0050 0.9487 0.0463 17 D 0.0051 0.9401 0.0548 18 A 0.0051 0.9426 0.0524 19 K 0.0050 0.9427 0.0522 20 K 0.0053 0.9253 0.0694 21 E 0.0077 0.8901 0.1022 22 F 0.0119 0.8186 0.1695 23 E 0.0130 0.7351 0.2519 24 M 0.0340 0.4995 0.4665 25 G 0.0236 0.2806 0.6958 26 L 0.0429 0.4294 0.5278 27 Y 0.0401 0.7422 0.2177 28 E 0.0117 0.9007 0.0876 29 R 0.0072 0.9335 0.0593 30 C 0.0058 0.9477 0.0465 31 C 0.0048 0.9549 0.0403 32 S 0.0048 0.9565 0.0387 33 T 0.0047 0.9560 0.0393 34 A 0.0047 0.9587 0.0365 35 Y 0.0047 0.9593 0.0360 36 Y 0.0047 0.9592 0.0360 37 A 0.0047 0.9579 0.0374 38 M 0.0047 0.9584 0.0369 39 F 0.0047 0.9587 0.0366 40 H 0.0048 0.9575 0.0377 41 A 0.0047 0.9592 0.0360 42 A 0.0047 0.9591 0.0362 43 K 0.0048 0.9584 0.0368 44 A 0.0048 0.9579 0.0373 45 M 0.0048 0.9567 0.0385 46 L 0.0049 0.9476 0.0475 47 L 0.0065 0.9150 0.0784 48 G 0.0145 0.8172 0.1683 49 Y 0.0423 0.4232 0.5345 50 G 0.0327 0.0678 0.8995 51 R 0.0764 0.0395 0.8842 52 D 0.1294 0.0364 0.8342 53 S 0.1037 0.1342 0.7621 54 K 0.0846 0.1865 0.7290 55 T 0.1158 0.2152 0.6690 56 H 0.1943 0.2144 0.5913 57 R 0.2214 0.3492 0.4295 58 G 0.3155 0.4139 0.2706 59 T 0.3144 0.4806 0.2050 60 I 0.3216 0.4850 0.1934 61 Y 0.2781 0.5055 0.2164 62 L 0.2571 0.4718 0.2711 63 I 0.1603 0.4726 0.3671 64 W 0.1125 0.4225 0.4650 65 E 0.1173 0.5569 0.3259 66 C 0.1853 0.5745 0.2402 67 R 0.2412 0.5194 0.2394 68 E 0.2105 0.5332 0.2563 69 E 0.1765 0.4925 0.3311 70 L 0.0868 0.3883 0.5249 71 G 0.0749 0.1568 0.7684 72 L 0.1798 0.1609 0.6593 73 S 0.2335 0.1823 0.5842 74 D 0.1708 0.2156 0.6136 75 D 0.1293 0.4253 0.4454 76 D 0.1793 0.4047 0.4160 77 C 0.2651 0.3492 0.3858 78 S 0.3354 0.2649 0.3997 79 K 0.3345 0.2995 0.3660 80 L 0.3215 0.3060 0.3725 81 S 0.2650 0.2862 0.4488 82 R 0.2006 0.2433 0.5561 83 A 0.0937 0.5199 0.3864 84 F 0.0678 0.6030 0.3293 85 D 0.0687 0.6259 0.3054 86 L 0.0555 0.6416 0.3029 87 R 0.0610 0.5745 0.3645 88 E 0.0393 0.4652 0.4955 89 E 0.0485 0.3116 0.6399 90 S 0.0757 0.1036 0.8207 91 D 0.0958 0.1152 0.7890 92 Y 0.0557 0.4333 0.5110 93 G 0.0449 0.5230 0.4321 94 I 0.0620 0.5462 0.3918 95 Y 0.1244 0.3623 0.5133 96 K 0.1952 0.2859 0.5188 97 E 0.2307 0.2530 0.5163 98 V 0.1518 0.2596 0.5885 99 S 0.0947 0.2194 0.6859 100 K 0.0052 0.9248 0.0699 101 D 0.0049 0.9398 0.0553 102 L 0.0049 0.9449 0.0502 103 A 0.0048 0.9498 0.0454 104 I 0.0047 0.9528 0.0425 105 K 0.0048 0.9471 0.0480 106 I 0.0050 0.9413 0.0536 107 L 0.0050 0.9493 0.0457 108 K 0.0049 0.9479 0.0472 109 D 0.0049 0.9449 0.0502 110 A 0.0048 0.9526 0.0426 111 E 0.0047 0.9576 0.0377 112 I 0.0047 0.9563 0.0389 113 F 0.0047 0.9566 0.0386 114 V 0.0047 0.9590 0.0363 115 Q 0.0047 0.9597 0.0356 116 K 0.0047 0.9590 0.0363 117 A 0.0047 0.9576 0.0377 118 K 0.0047 0.9565 0.0388 119 N 0.0048 0.9506 0.0446 120 A 0.0053 0.9384 0.0564 121 V 0.0079 0.8962 0.0958 122 N 0.0106 0.7514 0.2380 123 K 0.0272 0.4088 0.5640 124 N 0.0434 0.1255 0.8311 125 R 0.0416 0.0408 0.9176