# This file is the result of combining several RDB files, specifically # T0353.t06.dssp-ebghstl.rdb (weight 1.53986) # T0353.t06.stride-ebghtl.rdb (weight 1.24869) # T0353.t06.str2.rdb (weight 1.54758) # T0353.t06.alpha.rdb (weight 0.659012) # T0353.t04.dssp-ebghstl.rdb (weight 1.53986) # T0353.t04.stride-ebghtl.rdb (weight 1.24869) # T0353.t04.str2.rdb (weight 1.54758) # T0353.t04.alpha.rdb (weight 0.659012) # T0353.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0353.t2k.stride-ebghtl.rdb (weight 1.24869) # T0353.t2k.str2.rdb (weight 1.54758) # T0353.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 T0353.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.stride-ebghtl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.str2.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.alpha.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.stride-ebghtl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.str2.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.alpha.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 10 # # ============================================ # Comments from T0353.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 10 # # ============================================ # Comments from T0353.t2k.str2.rdb # ============================================ # TARGET T0353 # 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 T0353.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 10 # # ============================================ # Comments from T0353.t2k.alpha.rdb # ============================================ # TARGET T0353 # 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 T0353.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 10 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1762 0.0160 0.8078 2 Q 0.5315 0.0080 0.4606 3 I 0.7594 0.0062 0.2345 4 H 0.8605 0.0070 0.1326 5 V 0.8526 0.0222 0.1252 6 Y 0.7861 0.0263 0.1876 7 D 0.6684 0.0217 0.3098 8 T 0.5179 0.0288 0.4533 9 Y 0.6459 0.0276 0.3265 10 V 0.7205 0.0225 0.2570 11 K 0.7899 0.0146 0.1956 12 A 0.5370 0.0229 0.4401 13 K 0.1252 0.0915 0.7833 14 D 0.0589 0.0292 0.9119 15 G 0.1103 0.0326 0.8571 16 H 0.5359 0.0118 0.4523 17 V 0.8681 0.0042 0.1277 18 M 0.8809 0.0053 0.1138 19 H 0.8918 0.0051 0.1032 20 F 0.8674 0.0065 0.1261 21 D 0.8327 0.0219 0.1455 22 V 0.8715 0.0088 0.1197 23 F 0.8440 0.0098 0.1461 24 T 0.6323 0.0146 0.3531 25 D 0.2837 0.0214 0.6949 26 V 0.0460 0.1632 0.7908 27 R 0.0228 0.1953 0.7819 28 D 0.0361 0.2224 0.7415 29 D 0.0352 0.5566 0.4082 30 K 0.0148 0.8054 0.1797 31 K 0.0283 0.8443 0.1274 32 A 0.0218 0.9081 0.0701 33 I 0.0144 0.9363 0.0493 34 E 0.0126 0.9448 0.0427 35 F 0.0086 0.9511 0.0403 36 A 0.0062 0.9531 0.0407 37 K 0.0055 0.9560 0.0385 38 Q 0.0053 0.9538 0.0409 39 W 0.0051 0.9502 0.0447 40 L 0.0061 0.9282 0.0656 41 S 0.0065 0.8956 0.0979 42 S 0.0116 0.7937 0.1947 43 I 0.0469 0.4452 0.5079 44 G 0.0575 0.1517 0.7908 45 E 0.0971 0.1470 0.7559 46 E 0.1312 0.1803 0.6886 47 G 0.1091 0.2124 0.6785 48 A 0.1189 0.1495 0.7316 49 T 0.1690 0.0964 0.7346 50 V 0.2487 0.0674 0.6838 51 T 0.2049 0.0739 0.7212 52 S 0.1322 0.1873 0.6805 53 E 0.0648 0.3768 0.5583 54 E 0.1049 0.3698 0.5253 55 C 0.1449 0.3339 0.5212 56 R 0.1118 0.3726 0.5156 57 F 0.1182 0.4274 0.4544 58 C 0.1177 0.4027 0.4796 59 H 0.1190 0.3946 0.4864 60 S 0.0594 0.5696 0.3710 61 Q 0.0437 0.6187 0.3376 62 K 0.0485 0.4804 0.4710 63 A 0.0688 0.2915 0.6397 64 P 0.0554 0.2364 0.7082 65 D 0.0055 0.9313 0.0632 66 E 0.0047 0.9467 0.0485 67 V 0.0048 0.9549 0.0403 68 I 0.0047 0.9571 0.0382 69 E 0.0047 0.9556 0.0397 70 A 0.0048 0.9491 0.0461 71 I 0.0053 0.9392 0.0555 72 K 0.0059 0.9180 0.0761 73 Q 0.0112 0.7118 0.2770 74 N 0.0429 0.1820 0.7750 75 G 0.0592 0.0309 0.9099 76 Y 0.3303 0.0206 0.6491 77 F 0.7924 0.0106 0.1970 78 I 0.8675 0.0074 0.1251 79 Y 0.8404 0.0085 0.1512 80 K 0.7526 0.0163 0.2311 81 M 0.5643 0.0498 0.3859 82 E 0.3441 0.0679 0.5880 83 G 0.2032 0.0447 0.7521 84 C 0.1079 0.0328 0.8593 85 N 0.0432 0.0401 0.9167