# This file is the result of combining several RDB files, specifically # T0359.t06.dssp-ebghstl.rdb (weight 1.53986) # T0359.t06.stride-ebghtl.rdb (weight 1.24869) # T0359.t06.str2.rdb (weight 1.54758) # T0359.t06.alpha.rdb (weight 0.659012) # T0359.t04.dssp-ebghstl.rdb (weight 1.53986) # T0359.t04.stride-ebghtl.rdb (weight 1.24869) # T0359.t04.str2.rdb (weight 1.54758) # T0359.t04.alpha.rdb (weight 0.659012) # T0359.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0359.t2k.stride-ebghtl.rdb (weight 1.24869) # T0359.t2k.str2.rdb (weight 1.54758) # T0359.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 T0359.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0359 # 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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.stride-ebghtl.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.str2.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.alpha.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t04.stride-ebghtl.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t04.str2.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t04.alpha.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1518 # # ============================================ # Comments from T0359.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1518 # # ============================================ # Comments from T0359.t2k.str2.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1518 # # ============================================ # Comments from T0359.t2k.alpha.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1518 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1094 0.0475 0.8431 2 M 0.1608 0.0448 0.7945 3 S 0.2071 0.0354 0.7575 4 E 0.3472 0.0427 0.6101 5 T 0.5313 0.0283 0.4404 6 F 0.8055 0.0128 0.1817 7 D 0.8924 0.0058 0.1019 8 V 0.8956 0.0056 0.0988 9 E 0.9039 0.0054 0.0906 10 L 0.8500 0.0082 0.1418 11 T 0.7252 0.0206 0.2542 12 K 0.3561 0.0320 0.6118 13 N 0.0833 0.0719 0.8448 14 V 0.0735 0.0759 0.8506 15 Q 0.1285 0.0537 0.8178 16 G 0.2798 0.0523 0.6678 17 L 0.5997 0.0188 0.3814 18 G 0.8019 0.0117 0.1864 19 I 0.8846 0.0052 0.1102 20 T 0.8980 0.0046 0.0975 21 I 0.8914 0.0074 0.1012 22 A 0.8023 0.0202 0.1775 23 G 0.5452 0.0281 0.4266 24 Y 0.2737 0.0541 0.6722 25 I 0.2324 0.0758 0.6918 26 G 0.1900 0.0951 0.7149 27 D 0.1362 0.1167 0.7471 28 K 0.1035 0.1714 0.7251 29 K 0.0886 0.1794 0.7320 30 L 0.1039 0.1562 0.7399 31 E 0.1297 0.1180 0.7524 32 P 0.1964 0.0723 0.7312 33 S 0.2693 0.0512 0.6796 34 G 0.5497 0.0209 0.4294 35 I 0.8353 0.0072 0.1575 36 F 0.8979 0.0049 0.0972 37 V 0.9000 0.0041 0.0960 38 K 0.8274 0.0294 0.1432 39 S 0.7884 0.0086 0.2030 40 I 0.6637 0.0155 0.3207 41 T 0.2581 0.0193 0.7226 42 K 0.0506 0.0807 0.8687 43 S 0.0317 0.0439 0.9245 44 S 0.0832 0.0751 0.8417 45 A 0.0630 0.5829 0.3541 46 V 0.0449 0.7061 0.2489 47 E 0.0299 0.7609 0.2092 48 H 0.0435 0.6769 0.2797 49 D 0.0690 0.2621 0.6689 50 G 0.0382 0.0712 0.8906 51 R 0.1408 0.0409 0.8183 52 I 0.3602 0.0181 0.6216 53 Q 0.1048 0.0205 0.8747 54 I 0.0550 0.1168 0.8282 55 G 0.0763 0.0596 0.8642 56 D 0.3747 0.0468 0.5785 57 Q 0.8234 0.0108 0.1658 58 I 0.9000 0.0076 0.0925 59 I 0.9062 0.0070 0.0868 60 A 0.9003 0.0090 0.0907 61 V 0.8214 0.0178 0.1608 62 D 0.1533 0.0291 0.8176 63 G 0.0601 0.0544 0.8855 64 T 0.5664 0.0237 0.4099 65 N 0.5833 0.0243 0.3923 66 L 0.4434 0.0980 0.4586 67 Q 0.2157 0.1346 0.6497 68 G 0.0976 0.0969 0.8055 69 F 0.1880 0.0326 0.7794 70 T 0.1601 0.0368 0.8031 71 N 0.0054 0.9226 0.0721 72 Q 0.0048 0.9535 0.0417 73 Q 0.0047 0.9578 0.0375 74 A 0.0047 0.9593 0.0361 75 V 0.0047 0.9593 0.0360 76 E 0.0047 0.9571 0.0382 77 V 0.0048 0.9527 0.0425 78 L 0.0058 0.9375 0.0567 79 R 0.0073 0.8684 0.1243 80 H 0.0189 0.5977 0.3834 81 T 0.0556 0.1842 0.7602 82 G 0.0352 0.0793 0.8855 83 Q 0.0433 0.0569 0.8999 84 T 0.2797 0.0174 0.7029 85 V 0.7478 0.0045 0.2477 86 L 0.9042 0.0036 0.0923 87 L 0.9211 0.0033 0.0756 88 T 0.9210 0.0034 0.0757 89 L 0.9071 0.0033 0.0896 90 M 0.8247 0.0051 0.1702 91 R 0.5954 0.0075 0.3971 92 R 0.2220 0.0266 0.7514 93 G 0.0895 0.0403 0.8703 94 E 0.0724 0.0563 0.8713 95 T 0.0870 0.0421 0.8709 96 S 0.1104 0.0464 0.8432 97 V 0.0582 0.0429 0.8989