# This file is the result of combining several RDB files, specifically # T0335.t06.dssp-ebghstl.rdb (weight 1.53986) # T0335.t06.stride-ebghtl.rdb (weight 1.24869) # T0335.t06.str2.rdb (weight 1.54758) # T0335.t06.alpha.rdb (weight 0.659012) # T0335.t04.dssp-ebghstl.rdb (weight 1.53986) # T0335.t04.stride-ebghtl.rdb (weight 1.24869) # T0335.t04.str2.rdb (weight 1.54758) # T0335.t04.alpha.rdb (weight 0.659012) # T0335.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0335.t2k.stride-ebghtl.rdb (weight 1.24869) # T0335.t2k.str2.rdb (weight 1.54758) # T0335.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 T0335.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 53 # # ============================================ # Comments from T0335.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 53 # # ============================================ # Comments from T0335.t2k.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 53 # # ============================================ # Comments from T0335.t2k.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 53 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0515 0.0589 0.8896 2 I 0.0883 0.0791 0.8326 3 S 0.0532 0.2013 0.7454 4 N 0.0053 0.9287 0.0659 5 A 0.0054 0.9392 0.0554 6 K 0.0048 0.9533 0.0419 7 I 0.0047 0.9588 0.0365 8 A 0.0047 0.9575 0.0378 9 R 0.0047 0.9566 0.0387 10 I 0.0047 0.9588 0.0365 11 N 0.0047 0.9561 0.0392 12 E 0.0047 0.9543 0.0409 13 L 0.0049 0.9523 0.0428 14 A 0.0078 0.9369 0.0552 15 A 0.0073 0.9206 0.0721 16 K 0.0086 0.9180 0.0734 17 A 0.0085 0.9021 0.0894 18 K 0.0099 0.8153 0.1748 19 A 0.0207 0.6593 0.3200 20 G 0.0412 0.2984 0.6604 21 V 0.0361 0.1151 0.8488 22 I 0.0544 0.0358 0.9098 23 T 0.0468 0.0306 0.9226 24 E 0.0051 0.9079 0.0870 25 E 0.0048 0.9263 0.0689 26 E 0.0048 0.9353 0.0599 27 K 0.0047 0.9485 0.0468 28 A 0.0048 0.9423 0.0529 29 E 0.0048 0.9416 0.0536 30 Q 0.0049 0.9468 0.0483 31 Q 0.0049 0.9521 0.0430 32 K 0.0048 0.9533 0.0420 33 L 0.0048 0.9504 0.0447 34 R 0.0048 0.9565 0.0388 35 Q 0.0048 0.9554 0.0398 36 E 0.0049 0.9544 0.0407 37 Y 0.0048 0.9517 0.0435 38 L 0.0047 0.9524 0.0429 39 K 0.0050 0.9450 0.0501 40 G 0.0048 0.9270 0.0681 41 F 0.0048 0.9298 0.0654 42 R 0.0047 0.9456 0.0497 43 S 0.0049 0.9416 0.0535 44 S 0.0050 0.9282 0.0668 45 M 0.0051 0.9367 0.0582 46 K 0.0055 0.9297 0.0648 47 N 0.0090 0.8726 0.1184 48 T 0.0149 0.7847 0.2003 49 L 0.0948 0.5239 0.3813 50 K 0.0668 0.2825 0.6507 51 S 0.1524 0.1078 0.7397 52 V 0.4588 0.0186 0.5227 53 K 0.7405 0.0060 0.2535 54 I 0.8425 0.0052 0.1523 55 I 0.8237 0.0078 0.1685 56 D 0.3504 0.0144 0.6352 57 P 0.0140 0.1278 0.8582 58 E 0.0461 0.0301 0.9237 59 G 0.0392 0.0510 0.9097 60 N 0.1231 0.0356 0.8413 61 D 0.3733 0.0224 0.6043 62 V 0.2939 0.0191 0.6870 63 T 0.0884 0.0304 0.8812 64 P 0.0120 0.8690 0.1189 65 E 0.0067 0.9364 0.0569 66 K 0.0053 0.9485 0.0463 67 L 0.0047 0.9552 0.0401 68 K 0.0048 0.9547 0.0405 69 R 0.0047 0.9550 0.0403 70 E 0.0047 0.9521 0.0432 71 Q 0.0047 0.9508 0.0445 72 R 0.0048 0.9379 0.0573 73 N 0.0060 0.8935 0.1005 74 N 0.0404 0.4575 0.5021 75 K 0.0352 0.0860 0.8788 76 L 0.0624 0.0785 0.8591 77 H 0.1106 0.1069 0.7825 78 L 0.1279 0.1392 0.7329 79 E 0.1249 0.0972 0.7779 80 H 0.1434 0.0795 0.7771 81 H 0.0730 0.1832 0.7438 82 H 0.0732 0.1573 0.7695 83 H 0.0953 0.0988 0.8059 84 H 0.0614 0.1096 0.8290 85 H 0.0421 0.0521 0.9059