# This file is the result of combining several RDB files, specifically # T0251.t04.dssp-ebghstl.rdb (weight 1.53986) # T0251.t04.stride-ebghtl.rdb (weight 1.24869) # T0251.t04.str2.rdb (weight 1.54758) # T0251.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 T0251.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0251 # 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 T0251.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 4.47039 # # ============================================ # Comments from T0251.t04.stride-ebghtl.rdb # ============================================ # TARGET T0251 # 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 T0251.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 4.47039 # # ============================================ # Comments from T0251.t04.str2.rdb # ============================================ # TARGET T0251 # 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 T0251.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 4.47039 # # ============================================ # Comments from T0251.t04.alpha.rdb # ============================================ # TARGET T0251 # 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 T0251.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 4.47039 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3621 0.0082 0.6297 2 V 0.8373 0.0061 0.1566 3 V 0.8636 0.0073 0.1291 4 Y 0.7157 0.0352 0.2491 5 G 0.4944 0.0248 0.4808 6 A 0.4227 0.0911 0.4862 7 D 0.5255 0.1146 0.3599 8 V 0.6778 0.0839 0.2382 9 I 0.6979 0.0887 0.2134 10 C 0.5681 0.0906 0.3413 11 A 0.3130 0.2741 0.4129 12 S 0.1971 0.3195 0.4834 13 C 0.1538 0.3466 0.4995 14 V 0.1341 0.1832 0.6827 15 N 0.0993 0.1448 0.7559 16 A 0.0764 0.0323 0.8914 17 P 0.0811 0.0621 0.8568 18 T 0.0922 0.0585 0.8493 19 S 0.0215 0.6327 0.3458 20 K 0.0053 0.9207 0.0740 21 D 0.0065 0.9212 0.0723 22 I 0.0049 0.9480 0.0471 23 Y 0.0051 0.9503 0.0446 24 D 0.0049 0.9497 0.0454 25 W 0.0049 0.9441 0.0510 26 L 0.0049 0.9442 0.0509 27 Q 0.0047 0.9586 0.0367 28 P 0.0047 0.9571 0.0382 29 L 0.0050 0.9470 0.0480 30 L 0.0056 0.9077 0.0867 31 K 0.0079 0.7706 0.2215 32 R 0.0263 0.6402 0.3336 33 K 0.0800 0.3929 0.5272 34 Y 0.1006 0.0513 0.8482 35 P 0.0308 0.1087 0.8605 36 N 0.0366 0.0642 0.8991 37 I 0.2281 0.0314 0.7406 38 S 0.4423 0.0183 0.5394 39 F 0.7730 0.0051 0.2219 40 K 0.8613 0.0049 0.1338 41 Y 0.8811 0.0034 0.1155 42 T 0.8784 0.0066 0.1150 43 Y 0.9134 0.0036 0.0830 44 I 0.8895 0.0040 0.1064 45 D 0.8252 0.0046 0.1702 46 I 0.5425 0.0443 0.4131 47 T 0.2709 0.0571 0.6719 48 K 0.1406 0.0984 0.7609 49 D 0.0877 0.1316 0.7807 50 N 0.0577 0.2939 0.6485 51 D 0.0481 0.2782 0.6737 52 N 0.0661 0.2311 0.7027 53 L 0.0991 0.1838 0.7171 54 T 0.0792 0.2261 0.6946 55 D 0.0413 0.4583 0.5005 56 H 0.0282 0.5511 0.4208 57 D 0.0269 0.6848 0.2883 58 L 0.0092 0.9042 0.0865 59 Q 0.0103 0.9106 0.0791 60 F 0.0083 0.9269 0.0648 61 I 0.0080 0.9379 0.0541 62 E 0.0062 0.9368 0.0570 63 R 0.0074 0.9001 0.0924 64 I 0.0137 0.8113 0.1750 65 E 0.0216 0.6137 0.3647 66 Q 0.0199 0.5437 0.4364 67 D 0.0347 0.4909 0.4744 68 E 0.0524 0.4784 0.4692 69 L 0.1704 0.2825 0.5471 70 F 0.3117 0.1221 0.5662 71 Y 0.3091 0.0763 0.6147 72 P 0.3873 0.0583 0.5544 73 L 0.7579 0.0495 0.1926 74 I 0.8869 0.0196 0.0935 75 T 0.8899 0.0160 0.0941 76 M 0.7471 0.0382 0.2147 77 N 0.2285 0.0348 0.7367 78 D 0.0871 0.0657 0.8473 79 E 0.3975 0.0771 0.5254 80 Y 0.6914 0.0761 0.2325 81 V 0.5936 0.1004 0.3060 82 A 0.4540 0.1176 0.4285 83 D 0.2262 0.1603 0.6135 84 G 0.1685 0.1026 0.7289 85 Y 0.2723 0.1023 0.6255 86 I 0.3068 0.1957 0.4975 87 Q 0.2654 0.2581 0.4764 88 T 0.2092 0.4757 0.3152 89 K 0.1066 0.6923 0.2011 90 Q 0.1143 0.7422 0.1435 91 I 0.0795 0.8369 0.0836 92 T 0.0935 0.8411 0.0654 93 R 0.0497 0.8985 0.0519 94 F 0.0434 0.9016 0.0550 95 I 0.0457 0.8762 0.0781 96 D 0.0399 0.8499 0.1102 97 Q 0.0193 0.8567 0.1239 98 K 0.0300 0.7996 0.1704 99 L 0.0631 0.6494 0.2875 100 V 0.1020 0.4084 0.4896 101 N 0.0740 0.1988 0.7272 102 E 0.0464 0.0900 0.8636