# This file is the result of combining several RDB files, specifically # T0358.t06.dssp-ebghstl.rdb (weight 1.53986) # T0358.t06.stride-ebghtl.rdb (weight 1.24869) # T0358.t06.str2.rdb (weight 1.54758) # T0358.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 T0358.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 6.03747 # # ============================================ # Comments from T0358.t06.stride-ebghtl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 6.03747 # # ============================================ # Comments from T0358.t06.str2.rdb # ============================================ # TARGET T0358 # 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 T0358.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 6.03747 # # ============================================ # Comments from T0358.t06.alpha.rdb # ============================================ # TARGET T0358 # 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 T0358.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 6.03747 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0683 0.0498 0.8819 2 T 0.1597 0.0493 0.7910 3 Q 0.2660 0.0962 0.6378 4 S 0.3845 0.1287 0.4869 5 V 0.5123 0.1049 0.3829 6 L 0.5146 0.0527 0.4327 7 L 0.2054 0.0217 0.7729 8 P 0.0957 0.0221 0.8821 9 P 0.0526 0.0934 0.8540 10 G 0.0670 0.0717 0.8613 11 P 0.0677 0.2101 0.7221 12 F 0.1070 0.2485 0.6446 13 T 0.1028 0.3654 0.5318 14 R 0.0149 0.8466 0.1385 15 R 0.0277 0.8429 0.1293 16 Q 0.0448 0.8319 0.1233 17 A 0.0674 0.8313 0.1013 18 Q 0.1145 0.7845 0.1009 19 A 0.1897 0.7184 0.0920 20 V 0.2557 0.6443 0.1000 21 T 0.3437 0.5249 0.1314 22 T 0.3819 0.4025 0.2156 23 T 0.3983 0.2279 0.3738 24 Y 0.4654 0.1538 0.3808 25 S 0.3984 0.1202 0.4814 26 N 0.3841 0.0752 0.5407 27 I 0.5874 0.0249 0.3877 28 T 0.7245 0.0184 0.2571 29 L 0.7267 0.0307 0.2426 30 E 0.5504 0.0496 0.4000 31 D 0.2821 0.0419 0.6761 32 D 0.1015 0.0744 0.8241 33 Q 0.0606 0.0956 0.8438 34 G 0.0731 0.0918 0.8352 35 S 0.2062 0.0951 0.6987 36 H 0.5797 0.0378 0.3825 37 F 0.8204 0.0165 0.1631 38 R 0.8846 0.0126 0.1028 39 L 0.9208 0.0068 0.0724 40 V 0.9240 0.0064 0.0697 41 V 0.9169 0.0059 0.0773 42 R 0.8730 0.0099 0.1171 43 D 0.4608 0.0185 0.5208 44 T 0.0533 0.1323 0.8144 45 E 0.0485 0.0385 0.9130 46 G 0.0666 0.0348 0.8986 47 R 0.3453 0.0268 0.6279 48 M 0.8603 0.0057 0.1340 49 V 0.8959 0.0099 0.0942 50 W 0.9074 0.0104 0.0822 51 R 0.8625 0.0234 0.1142 52 A 0.7563 0.0497 0.1940 53 W 0.4787 0.0895 0.4318 54 N 0.2696 0.0649 0.6655 55 F 0.1409 0.0583 0.8008 56 E 0.0905 0.0419 0.8676 57 P 0.0398 0.1795 0.7808 58 D 0.0424 0.1667 0.7908 59 A 0.0512 0.3478 0.6010 60 G 0.0339 0.3627 0.6034 61 E 0.0251 0.6344 0.3406 62 G 0.0315 0.7323 0.2362 63 L 0.0229 0.8354 0.1417 64 N 0.0205 0.8599 0.1196 65 R 0.0207 0.8914 0.0878 66 Y 0.0332 0.8783 0.0884 67 I 0.0614 0.8371 0.1014 68 R 0.0605 0.7747 0.1647 69 T 0.0382 0.6835 0.2784 70 S 0.0492 0.3498 0.6011 71 G 0.0633 0.1259 0.8108 72 I 0.1995 0.1082 0.6922 73 R 0.2603 0.1297 0.6100 74 T 0.1477 0.2690 0.5833 75 D 0.1071 0.2511 0.6418 76 T 0.1233 0.3334 0.5433 77 A 0.1685 0.3540 0.4776 78 T 0.1771 0.4037 0.4192 79 R 0.2029 0.4623 0.3347 80 L 0.2025 0.4623 0.3351 81 E 0.1815 0.4273 0.3912 82 H 0.1458 0.4163 0.4379 83 H 0.1319 0.3352 0.5329 84 H 0.1153 0.2736 0.6111 85 H 0.1014 0.2029 0.6956 86 H 0.0841 0.1243 0.7916 87 H 0.0538 0.0381 0.9082