# This file is the result of combining several RDB files, specifically # T0272.t04.dssp-ebghstl.rdb (weight 1.53986) # T0272.t04.stride-ebghtl.rdb (weight 1.24869) # T0272.t04.str2.rdb (weight 1.54758) # T0272.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 T0272.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 2 # # ============================================ # Comments from T0272.t04.stride-ebghtl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 2 # # ============================================ # Comments from T0272.t04.str2.rdb # ============================================ # TARGET T0272 # 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 T0272.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 2 # # ============================================ # Comments from T0272.t04.alpha.rdb # ============================================ # TARGET T0272 # 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 T0272.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0778 0.1237 0.7984 2 T 0.1039 0.1538 0.7424 3 G 0.1222 0.1001 0.7777 4 K 0.2660 0.1291 0.6049 5 R 0.5051 0.1599 0.3351 6 V 0.5106 0.1815 0.3078 7 A 0.4932 0.1821 0.3247 8 L 0.3614 0.1615 0.4771 9 K 0.2117 0.1441 0.6442 10 T 0.0939 0.0500 0.8561 11 P 0.0569 0.3935 0.5497 12 A 0.0125 0.8637 0.1238 13 E 0.0150 0.8997 0.0853 14 K 0.0203 0.9134 0.0662 15 V 0.0254 0.9170 0.0577 16 A 0.0207 0.9254 0.0539 17 W 0.0256 0.9208 0.0536 18 L 0.0344 0.9022 0.0634 19 E 0.0291 0.8977 0.0731 20 R 0.0363 0.8572 0.1065 21 R 0.0466 0.7954 0.1580 22 L 0.0506 0.7220 0.2273 23 E 0.0743 0.6154 0.3103 24 E 0.0665 0.4110 0.5225 25 G 0.0659 0.1353 0.7988 26 G 0.1515 0.0797 0.7688 27 F 0.4854 0.0617 0.4529 28 R 0.6983 0.0582 0.2435 29 L 0.6861 0.0673 0.2465 30 L 0.5711 0.0849 0.3440 31 E 0.3147 0.1030 0.5823 32 G 0.1054 0.0864 0.8083 33 E 0.1529 0.0907 0.7563 34 R 0.1824 0.0538 0.7638 35 G 0.1439 0.0287 0.8274 36 P 0.2242 0.0475 0.7283 37 W 0.6566 0.0671 0.2763 38 V 0.8173 0.0428 0.1399 39 Q 0.8631 0.0353 0.1016 40 I 0.8141 0.0505 0.1354 41 L 0.5881 0.0928 0.3191 42 Q 0.2280 0.3367 0.4353 43 D 0.0748 0.4915 0.4337 44 T 0.0710 0.5624 0.3666 45 F 0.1524 0.6051 0.2425 46 L 0.2515 0.5610 0.1875 47 E 0.2778 0.5509 0.1713 48 V 0.2695 0.5428 0.1877 49 R 0.3176 0.4794 0.2029 50 R 0.3257 0.3828 0.2915 51 K 0.1235 0.3078 0.5688 52 K 0.0658 0.3110 0.6232 53 D 0.0663 0.1221 0.8116 54 G 0.0419 0.1158 0.8423 55 E 0.1134 0.3245 0.5620 56 E 0.2625 0.3193 0.4182 57 A 0.1980 0.2762 0.5258 58 G 0.1956 0.1534 0.6510 59 K 0.3589 0.1015 0.5396 60 L 0.5274 0.1472 0.3254 61 L 0.6262 0.0778 0.2960 62 Q 0.8034 0.0536 0.1430 63 V 0.8373 0.0480 0.1148 64 Q 0.8047 0.0692 0.1261 65 A 0.8710 0.0363 0.0927 66 V 0.8722 0.0360 0.0917 67 L 0.8611 0.0403 0.0986 68 F 0.8029 0.0436 0.1536 69 E 0.5547 0.0664 0.3789 70 G 0.3650 0.0444 0.5905 71 R 0.5620 0.0529 0.3850 72 L 0.7406 0.0327 0.2266 73 E 0.7713 0.0319 0.1968 74 V 0.7902 0.0211 0.1886 75 V 0.5127 0.0296 0.4576 76 D 0.1569 0.0146 0.8285 77 P 0.0059 0.8756 0.1186 78 E 0.0050 0.9344 0.0606 79 R 0.0049 0.9438 0.0512 80 A 0.0053 0.9421 0.0526 81 L 0.0052 0.9498 0.0449 82 A 0.0049 0.9477 0.0474 83 T 0.0051 0.9438 0.0511 84 L 0.0053 0.9319 0.0627 85 R 0.0071 0.8985 0.0944 86 R 0.0382 0.5913 0.3705 87 G 0.0323 0.2496 0.7181 88 V 0.0780 0.1039 0.8181 89 G 0.0830 0.0851 0.8319 90 P 0.0556 0.4033 0.5411 91 G 0.0438 0.5555 0.4007 92 K 0.0618 0.6016 0.3366 93 A 0.1233 0.5457 0.3310 94 L 0.1420 0.3591 0.4990 95 G 0.1698 0.1679 0.6623 96 L 0.2477 0.1277 0.6246 97 G 0.3931 0.1076 0.4994 98 L 0.6194 0.0931 0.2875 99 L 0.6888 0.0594 0.2519 100 S 0.6355 0.0511 0.3133 101 V 0.4856 0.0520 0.4624 102 A 0.2092 0.0187 0.7721 103 P 0.0933 0.0481 0.8587