# This file is the result of combining several RDB files, specifically # T0262.t04.dssp-ebghstl.rdb (weight 1.53986) # T0262.t04.stride-ebghtl.rdb (weight 1.24869) # T0262.t04.str2.rdb (weight 1.54758) # T0262.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 T0262.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 T0262.t04.stride-ebghtl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 T0262.t04.str2.rdb # ============================================ # TARGET T0262 # 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 T0262.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 T0262.t04.alpha.rdb # ============================================ # TARGET T0262 # 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 T0262.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 M 0.0631 0.0131 0.9238 2 P 0.0672 0.0250 0.9079 3 S 0.0675 0.0955 0.8371 4 S 0.0398 0.3370 0.6231 5 S 0.0437 0.4867 0.4696 6 Q 0.0825 0.5079 0.4096 7 Y 0.1593 0.4624 0.3783 8 R 0.1909 0.4346 0.3745 9 R 0.2420 0.3476 0.4104 10 Y 0.2332 0.2174 0.5494 11 Q 0.1882 0.1226 0.6891 12 D 0.1022 0.0239 0.8739 13 P 0.0244 0.1309 0.8447 14 H 0.0450 0.0874 0.8676 15 H 0.0883 0.0451 0.8666 16 P 0.0549 0.0875 0.8577 17 S 0.1073 0.0711 0.8216 18 I 0.1131 0.0194 0.8675 19 P 0.1195 0.0212 0.8593 20 T 0.1506 0.0181 0.8313 21 P 0.1366 0.0895 0.7739 22 T 0.1899 0.1709 0.6391 23 T 0.3100 0.1939 0.4961 24 L 0.3405 0.1875 0.4719 25 F 0.2871 0.1249 0.5879 26 S 0.2128 0.0975 0.6897 27 Q 0.1152 0.0534 0.8313 28 P 0.0936 0.1541 0.7523 29 S 0.1628 0.2602 0.5769 30 L 0.2660 0.3762 0.3578 31 E 0.3559 0.3966 0.2475 32 I 0.3979 0.3767 0.2254 33 L 0.2775 0.3389 0.3835 34 G 0.1243 0.2203 0.6554 35 G 0.0595 0.2609 0.6795 36 G 0.0781 0.3855 0.5365 37 V 0.0753 0.6229 0.3017 38 A 0.0381 0.7507 0.2113 39 E 0.0249 0.6926 0.2825 40 E 0.0367 0.5623 0.4009 41 L 0.0703 0.2302 0.6995 42 P 0.0328 0.4620 0.5052 43 E 0.0838 0.5322 0.3840 44 L 0.2163 0.5012 0.2825 45 A 0.3593 0.4107 0.2300 46 L 0.4137 0.3113 0.2750 47 C 0.4163 0.1689 0.4148 48 C 0.3646 0.0832 0.5522 49 D 0.1043 0.0560 0.8397 50 G 0.1310 0.0486 0.8204 51 T 0.5701 0.0263 0.4037 52 V 0.8386 0.0161 0.1453 53 V 0.7839 0.0256 0.1905 54 E 0.6117 0.0444 0.3439 55 G 0.2858 0.0374 0.6768 56 R 0.2477 0.0587 0.6936 57 S 0.2373 0.1098 0.6529 58 N 0.1645 0.1551 0.6804 59 C 0.2282 0.1591 0.6127 60 R 0.3358 0.1861 0.4781 61 C 0.4074 0.1566 0.4360 62 K 0.4468 0.1447 0.4086 63 A 0.5089 0.1426 0.3486 64 R 0.5492 0.1386 0.3122 65 A 0.7441 0.0640 0.1918 66 V 0.7810 0.0400 0.1790 67 L 0.5696 0.0281 0.4023 68 P 0.2182 0.0809 0.7009 69 G 0.0980 0.0423 0.8597 70 G 0.1902 0.0532 0.7567 71 M 0.4387 0.0380 0.5233 72 R 0.8171 0.0301 0.1529 73 V 0.8388 0.0321 0.1291 74 R 0.7867 0.0787 0.1346 75 L 0.6331 0.1684 0.1985 76 S 0.3540 0.2732 0.3727 77 K 0.2223 0.4056 0.3721 78 T 0.2297 0.4922 0.2781 79 L 0.1533 0.6695 0.1772 80 A 0.1295 0.7099 0.1606 81 G 0.1279 0.6961 0.1760 82 I 0.1791 0.6415 0.1794 83 L 0.2067 0.5308 0.2625 84 R 0.1749 0.3330 0.4921 85 H 0.0897 0.0890 0.8213