# This file is the result of combining several RDB files, specifically # T0344.t06.dssp-ebghstl.rdb (weight 1.53986) # T0344.t06.stride-ebghtl.rdb (weight 1.24869) # T0344.t06.str2.rdb (weight 1.54758) # T0344.t06.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 T0344.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.2843 0.0465 0.6692 2 I 0.6352 0.0499 0.3148 3 I 0.6643 0.0616 0.2741 4 G 0.5477 0.0418 0.4105 5 L 0.3699 0.0437 0.5864 6 P 0.3150 0.0753 0.6097 7 R 0.3939 0.1173 0.4888 8 Y 0.6399 0.0565 0.3036 9 M 0.7692 0.0143 0.2164 10 E 0.8603 0.0076 0.1321 11 V 0.8545 0.0061 0.1395 12 N 0.8612 0.0054 0.1334 13 I 0.7101 0.0114 0.2785 14 K 0.3981 0.0286 0.5733 15 D 0.0574 0.0479 0.8947 16 G 0.0562 0.0394 0.9044 17 K 0.5628 0.0236 0.4136 18 I 0.8286 0.0083 0.1631 19 I 0.7013 0.0305 0.2682 20 G 0.4917 0.0342 0.4741 21 R 0.4519 0.0463 0.5018 22 S 0.4911 0.0307 0.4782 23 L 0.3881 0.0261 0.5857 24 D 0.2088 0.0115 0.7797 25 P 0.0255 0.2817 0.6929 26 R 0.0323 0.2594 0.7084 27 E 0.0984 0.2527 0.6489 28 G 0.1148 0.0936 0.7916 29 G 0.2217 0.0744 0.7040 30 L 0.5400 0.0563 0.4037 31 Y 0.5822 0.0481 0.3697 32 G 0.5736 0.0289 0.3975 33 S 0.7018 0.0228 0.2754 34 A 0.7980 0.0193 0.1827 35 E 0.8480 0.0139 0.1382 36 V 0.8213 0.0133 0.1654 37 S 0.7342 0.0148 0.2510 38 V 0.4003 0.0221 0.5776 39 P 0.1744 0.0676 0.7580 40 E 0.0719 0.0890 0.8391 41 G 0.1334 0.0614 0.8053 42 V 0.4840 0.0142 0.5017 43 K 0.7580 0.0123 0.2296 44 W 0.8504 0.0142 0.1354 45 E 0.8470 0.0193 0.1337 46 I 0.7971 0.0258 0.1771 47 Y 0.4870 0.0167 0.4963 48 P 0.1858 0.0473 0.7668 49 N 0.1073 0.0604 0.8323 50 P 0.0258 0.6072 0.3669 51 V 0.0354 0.6895 0.2751 52 A 0.0836 0.7044 0.2120 53 R 0.1368 0.6682 0.1950 54 R 0.3026 0.5054 0.1919 55 F 0.4488 0.3896 0.1616 56 M 0.5349 0.3484 0.1167 57 I 0.6137 0.2958 0.0905 58 F 0.6144 0.2813 0.1042 59 E 0.6391 0.2510 0.1100 60 I 0.5866 0.2551 0.1583 61 F 0.4448 0.1996 0.3556 62 S 0.2924 0.1299 0.5777 63 K 0.1231 0.1142 0.7627 64 R 0.0501 0.0325 0.9174