# This file is the result of combining several RDB files, specifically # TR462.t04.str2.rdb (weight 1.54425) # TR462.t04.str4.rdb (weight 0.924988) # TR462.t04.pb.rdb (weight 0.789901) # TR462.t04.bys.rdb (weight 0.748322) # TR462.t04.alpha.rdb (weight 0.678173) # 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 TR462.t04.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-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 TR462.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 TR462.t04.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR462.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 TR462.t04.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR462.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 TR462.t04.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR462.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 TR462.t04.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-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 TR462.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 E 0.2755 0.1299 0.5946 2 L 0.3578 0.0388 0.6033 3 P 0.4293 0.0713 0.4994 4 L 0.6598 0.0509 0.2892 5 I 0.7139 0.0301 0.2560 6 L 0.6751 0.0313 0.2936 7 A 0.5031 0.0651 0.4317 8 D 0.2718 0.1405 0.5877 9 D 0.1417 0.1311 0.7272 10 G 0.1448 0.0927 0.7625 11 T 0.3745 0.0863 0.5392 12 Y 0.5805 0.0672 0.3523 13 E 0.6560 0.0703 0.2737 14 I 0.6391 0.0853 0.2756 15 T 0.5877 0.1160 0.2963 16 K 0.5448 0.1306 0.3246 17 L 0.3609 0.2105 0.4286 18 N 0.2031 0.1617 0.6352 19 G 0.1192 0.1361 0.7447 20 G 0.1460 0.1648 0.6892 21 R 0.2437 0.2832 0.4731 22 R 0.3424 0.3486 0.3090 23 F 0.3978 0.3574 0.2448 24 L 0.4487 0.3428 0.2084 25 F 0.4456 0.3602 0.1942 26 R 0.3943 0.3892 0.2166 27 M 0.2688 0.4449 0.2863 28 K 0.1667 0.4711 0.3622 29 N 0.1372 0.3897 0.4732 30 L 0.1642 0.2533 0.5825 31 G 0.1929 0.1760 0.6311 32 I 0.2754 0.2082 0.5165 33 E 0.2928 0.2165 0.4907 34 S 0.1941 0.1462 0.6596 35 G 0.1379 0.0916 0.7704 36 K 0.3462 0.0705 0.5834 37 K 0.5902 0.0448 0.3650 38 I 0.6818 0.0282 0.2900 39 Q 0.6713 0.0275 0.3012 40 V 0.6359 0.0452 0.3189 41 S 0.4153 0.0746 0.5100 42 G 0.2633 0.0749 0.6618 43 R 0.4048 0.0800 0.5152 44 R 0.5799 0.0680 0.3522 45 Y 0.6856 0.0467 0.2677 46 Y 0.7052 0.0382 0.2566 47 I 0.6536 0.0512 0.2953 48 E 0.4333 0.0763 0.4904 49 G 0.2374 0.0805 0.6821 50 R 0.3982 0.0980 0.5039 51 E 0.5497 0.0798 0.3705 52 I 0.5570 0.0813 0.3617 53 D 0.4140 0.0986 0.4874 54 L 0.2668 0.2188 0.5144 55 G 0.1805 0.1656 0.6538 56 Y 0.1919 0.1857 0.6224 57 G 0.1811 0.1772 0.6416 58 E 0.2297 0.2626 0.5077 59 A 0.3351 0.2292 0.4357 60 T 0.3925 0.2139 0.3936 61 K 0.5715 0.1369 0.2916 62 I 0.6555 0.1002 0.2443 63 W 0.6868 0.0716 0.2416 64 V 0.6769 0.0841 0.2390 65 R 0.5945 0.1171 0.2884 66 R 0.5354 0.0993 0.3653 67 V 0.3886 0.1059 0.5055