# This file is the result of combining several RDB files, specifically # T0239.t04.dssp-ebghstl.rdb (weight 1.53986) # T0239.t04.stride-ebghtl.rdb (weight 1.24869) # T0239.t04.str2.rdb (weight 1.54758) # T0239.t04.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 T0239.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0239 # Using neural net t04-2621-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 T0239.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 1 # # ============================================ # Comments from T0239.t04.stride-ebghtl.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ # Comments from T0239.t04.str2.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ # Comments from T0239.t04.alpha.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1528 0.2312 0.6160 2 K 0.2185 0.2259 0.5556 3 K 0.3494 0.1905 0.4601 4 H 0.6113 0.0833 0.3054 5 I 0.8309 0.0336 0.1356 6 I 0.8661 0.0312 0.1026 7 I 0.8309 0.0335 0.1356 8 K 0.6963 0.0405 0.2632 9 T 0.5632 0.0399 0.3970 10 I 0.2303 0.0230 0.7467 11 P 0.1246 0.0379 0.8375 12 K 0.0827 0.2308 0.6865 13 K 0.0629 0.5341 0.4031 14 E 0.0836 0.5947 0.3217 15 E 0.1360 0.5764 0.2876 16 I 0.2297 0.4911 0.2792 17 I 0.2260 0.4256 0.3483 18 S 0.1713 0.3252 0.5034 19 R 0.0590 0.4755 0.4655 20 D 0.0827 0.4293 0.4880 21 L 0.0843 0.5595 0.3562 22 C 0.1561 0.3980 0.4459 23 D 0.1550 0.3486 0.4964 24 C 0.4053 0.2542 0.3405 25 I 0.6441 0.1585 0.1974 26 Y 0.7798 0.0785 0.1417 27 Y 0.7375 0.0589 0.2036 28 Y 0.5760 0.0523 0.3717 29 D 0.1644 0.0685 0.7672 30 N 0.0719 0.0678 0.8603 31 S 0.3999 0.0478 0.5523 32 V 0.7768 0.0163 0.2069 33 I 0.8347 0.0124 0.1530 34 C 0.7539 0.0168 0.2294 35 K 0.5675 0.0212 0.4114 36 P 0.4472 0.0281 0.5247 37 I 0.2997 0.0429 0.6574 38 G 0.1549 0.0199 0.8252 39 P 0.0992 0.1080 0.7928 40 S 0.1393 0.1174 0.7433 41 K 0.4953 0.0908 0.4139 42 V 0.7667 0.0332 0.2001 43 Y 0.8376 0.0312 0.1312 44 V 0.7853 0.0486 0.1661 45 S 0.5345 0.0730 0.3925 46 T 0.3097 0.1022 0.5881 47 S 0.2244 0.1518 0.6239 48 L 0.0603 0.6744 0.2653 49 E 0.0348 0.7183 0.2468 50 N 0.0327 0.7247 0.2426 51 L 0.0122 0.8711 0.1167 52 E 0.0083 0.9148 0.0770 53 K 0.0091 0.9161 0.0748 54 C 0.0108 0.9148 0.0743 55 L 0.0177 0.8915 0.0907 56 Q 0.0201 0.8607 0.1192 57 L 0.0164 0.8788 0.1048 58 H 0.0150 0.8734 0.1116 59 Y 0.0209 0.8552 0.1239 60 F 0.0184 0.8948 0.0868 61 K 0.0135 0.9183 0.0681 62 K 0.0209 0.9074 0.0717 63 L 0.0196 0.8956 0.0847 64 V 0.0285 0.8722 0.0993 65 K 0.0278 0.7982 0.1740 66 N 0.0454 0.6525 0.3022 67 I 0.0935 0.6159 0.2907 68 E 0.1734 0.5405 0.2862 69 I 0.2439 0.5737 0.1824 70 F 0.2193 0.5570 0.2237 71 D 0.1445 0.6173 0.2382 72 E 0.1098 0.6816 0.2086 73 V 0.1149 0.6348 0.2503 74 H 0.1117 0.4679 0.4204 75 N 0.0685 0.2425 0.6890 76 S 0.0713 0.1228 0.8058 77 K 0.0759 0.0385 0.8857 78 P 0.0515 0.1338 0.8147 79 N 0.0676 0.1243 0.8081 80 C 0.1393 0.1294 0.7312 81 D 0.1239 0.1378 0.7382 82 K 0.4042 0.1117 0.4841 83 C 0.7233 0.0368 0.2399 84 L 0.8745 0.0158 0.1097 85 I 0.9009 0.0123 0.0868 86 V 0.8870 0.0174 0.0956 87 E 0.8708 0.0162 0.1130 88 I 0.7068 0.0459 0.2474 89 G 0.2541 0.0374 0.7085 90 G 0.3431 0.0354 0.6215 91 V 0.8134 0.0185 0.1682 92 Y 0.8817 0.0125 0.1058 93 F 0.8963 0.0124 0.0913 94 V 0.8774 0.0195 0.1031 95 R 0.8273 0.0294 0.1432 96 R 0.7294 0.0289 0.2417 97 V 0.3606 0.0415 0.5978 98 N 0.1014 0.0270 0.8716