# This file is the result of combining several RDB files, specifically # T0330.t06.dssp-ebghstl.rdb (weight 1.53986) # T0330.t06.stride-ebghtl.rdb (weight 1.24869) # T0330.t06.str2.rdb (weight 1.54758) # T0330.t06.alpha.rdb (weight 0.659012) # T0330.t04.dssp-ebghstl.rdb (weight 1.53986) # T0330.t04.stride-ebghtl.rdb (weight 1.24869) # T0330.t04.str2.rdb (weight 1.54758) # T0330.t04.alpha.rdb (weight 0.659012) # T0330.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0330.t2k.stride-ebghtl.rdb (weight 1.24869) # T0330.t2k.str2.rdb (weight 1.54758) # T0330.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 T0330.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 12 # # ============================================ # Comments from T0330.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 12 # # ============================================ # Comments from T0330.t2k.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 12 # # ============================================ # Comments from T0330.t2k.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 12 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.1198 0.0379 0.8423 2 K 0.2433 0.0333 0.7234 3 V 0.1494 0.1441 0.7065 4 E 0.0737 0.2206 0.7057 5 S 0.0603 0.4489 0.4908 6 M 0.0389 0.6551 0.3060 7 N 0.0356 0.6856 0.2789 8 R 0.0080 0.9033 0.0887 9 R 0.0058 0.9351 0.0591 10 V 0.0052 0.9497 0.0451 11 L 0.0047 0.9563 0.0389 12 A 0.0047 0.9593 0.0360 13 D 0.0047 0.9589 0.0364 14 A 0.0047 0.9572 0.0381 15 L 0.0048 0.9544 0.0408 16 I 0.0052 0.9430 0.0517 17 E 0.0068 0.9106 0.0826 18 V 0.0171 0.8444 0.1385 19 Y 0.0581 0.6696 0.2723 20 G 0.0461 0.2431 0.7108 21 T 0.0847 0.1147 0.8006 22 E 0.1596 0.1015 0.7389 23 G 0.1378 0.0931 0.7691 24 S 0.1173 0.0614 0.8214 25 T 0.0904 0.2486 0.6610 26 G 0.0820 0.2538 0.6642 27 S 0.1358 0.2547 0.6094 28 H 0.2123 0.1481 0.6396 29 D 0.1749 0.1801 0.6450 30 F 0.1218 0.2424 0.6358 31 S 0.0988 0.2361 0.6652 32 G 0.0862 0.1811 0.7327 33 K 0.0799 0.2426 0.6775 34 M 0.1180 0.3230 0.5590 35 D 0.0669 0.5034 0.4297 36 G 0.0116 0.9001 0.0882 37 A 0.0132 0.9311 0.0557 38 I 0.0147 0.9400 0.0453 39 I 0.0141 0.9408 0.0450 40 Y 0.0079 0.9487 0.0433 41 E 0.0069 0.9527 0.0404 42 V 0.0057 0.9502 0.0442 43 L 0.0059 0.9406 0.0535 44 S 0.0064 0.9057 0.0880 45 N 0.0084 0.7754 0.2161 46 V 0.0424 0.3800 0.5776 47 G 0.0427 0.0446 0.9127 48 L 0.0690 0.0166 0.9144 49 E 0.0559 0.0165 0.9276 50 R 0.0167 0.7867 0.1965 51 A 0.0090 0.8474 0.1436 52 E 0.0085 0.8963 0.0951 53 I 0.0072 0.9148 0.0780 54 A 0.0053 0.9046 0.0901 55 D 0.0056 0.8394 0.1550 56 K 0.0072 0.8479 0.1449 57 F 0.0119 0.8626 0.1255 58 D 0.0052 0.9305 0.0643 59 K 0.0051 0.9419 0.0530 60 A 0.0049 0.9495 0.0457 61 K 0.0048 0.9535 0.0417 62 E 0.0049 0.9536 0.0416 63 T 0.0049 0.9491 0.0461 64 Y 0.0048 0.9520 0.0432 65 I 0.0047 0.9572 0.0381 66 A 0.0048 0.9551 0.0401 67 L 0.0049 0.9487 0.0464 68 F 0.0053 0.9382 0.0565 69 R 0.0054 0.9179 0.0766 70 E 0.0109 0.8154 0.1737 71 R 0.0204 0.5666 0.4130 72 A 0.0830 0.2027 0.7144 73 R 0.0603 0.0442 0.8955 74 R 0.0161 0.6478 0.3361 75 E 0.0207 0.6371 0.3422 76 D 0.0602 0.5878 0.3520 77 I 0.2881 0.1205 0.5914 78 T 0.2089 0.0550 0.7360 79 L 0.0645 0.0326 0.9028