# This file is the result of combining several RDB files, specifically # T0396.t06.str2.rdb (weight 1.54425) # T0396.t06.str4.rdb (weight 0.924988) # T0396.t06.pb.rdb (weight 0.789901) # T0396.t06.bys.rdb (weight 0.748322) # T0396.t06.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 T0396.t06.str2.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-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 T0396.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 114.473 # # ============================================ # Comments from T0396.t06.str4.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t06-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 T0396.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 114.473 # # ============================================ # Comments from T0396.t06.pb.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t06-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 T0396.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 114.473 # # ============================================ # Comments from T0396.t06.bys.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t06-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 T0396.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 114.473 # # ============================================ # Comments from T0396.t06.alpha.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-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 T0396.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 114.473 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1500 0.0924 0.7576 2 S 0.2012 0.0936 0.7051 3 M 0.1531 0.4029 0.4440 4 L 0.1310 0.4701 0.3989 5 H 0.1607 0.3926 0.4468 6 W 0.1864 0.2654 0.5482 7 G 0.1359 0.2326 0.6315 8 P 0.0349 0.6819 0.2832 9 K 0.0171 0.8334 0.1495 10 Y 0.0123 0.9061 0.0816 11 W 0.0136 0.9108 0.0757 12 R 0.0101 0.9168 0.0731 13 S 0.0103 0.9161 0.0737 14 L 0.0100 0.9153 0.0747 15 H 0.0124 0.9081 0.0795 16 L 0.0212 0.8857 0.0931 17 Y 0.0404 0.8375 0.1221 18 A 0.0805 0.7504 0.1691 19 I 0.1297 0.6198 0.2504 20 F 0.1621 0.4097 0.4282 21 F 0.2129 0.1459 0.6412 22 S 0.1290 0.1993 0.6717 23 D 0.1030 0.1612 0.7358 24 A 0.1915 0.0576 0.7509 25 P 0.1584 0.1380 0.7036 26 S 0.1677 0.1119 0.7204 27 W 0.0288 0.6587 0.3125 28 K 0.0242 0.7445 0.2313 29 E 0.0264 0.8247 0.1489 30 K 0.0122 0.8841 0.1037 31 Y 0.0085 0.9118 0.0797 32 E 0.0083 0.9226 0.0691 33 A 0.0083 0.9232 0.0685 34 I 0.0083 0.9237 0.0680 35 Q 0.0083 0.9244 0.0674 36 W 0.0083 0.9241 0.0676 37 I 0.0083 0.9232 0.0685 38 L 0.0084 0.9183 0.0733 39 N 0.0095 0.8905 0.1000 40 F 0.0149 0.8567 0.1284 41 I 0.0198 0.8202 0.1599 42 E 0.0386 0.7117 0.2498 43 S 0.0769 0.5428 0.3803 44 L 0.1920 0.1661 0.6419 45 P 0.1627 0.1518 0.6855 46 C 0.1067 0.2994 0.5939 47 T 0.0323 0.6664 0.3013 48 R 0.0295 0.7450 0.2254 49 C 0.0374 0.7859 0.1767 50 Q 0.0101 0.8883 0.1017 51 H 0.0086 0.9046 0.0868 52 H 0.0087 0.9083 0.0830 53 A 0.0084 0.9171 0.0744 54 F 0.0084 0.9156 0.0760 55 S 0.0084 0.9154 0.0762 56 Y 0.0093 0.8963 0.0944 57 L 0.0137 0.8524 0.1339 58 T 0.0181 0.7651 0.2168 59 K 0.0526 0.4992 0.4482 60 N 0.1655 0.1040 0.7305 61 P 0.1336 0.1916 0.6748 62 L 0.1810 0.1923 0.6267 63 T 0.2782 0.1391 0.5828 64 L 0.2935 0.1281 0.5784 65 N 0.2302 0.0954 0.6744 66 N 0.1923 0.0462 0.7615 67 S 0.0370 0.5377 0.4253 68 E 0.0205 0.7375 0.2420 69 D 0.0274 0.7988 0.1738 70 F 0.0293 0.8494 0.1212 71 Q 0.0233 0.8800 0.0967 72 Y 0.0317 0.8817 0.0866 73 W 0.0318 0.8780 0.0901 74 T 0.0472 0.8597 0.0931 75 F 0.0358 0.8712 0.0930 76 A 0.0320 0.8678 0.1003 77 F 0.0287 0.8452 0.1261 78 H 0.0273 0.8236 0.1490 79 N 0.0248 0.7973 0.1779 80 N 0.0303 0.7937 0.1760 81 V 0.0403 0.7980 0.1617 82 N 0.0502 0.7367 0.2131 83 N 0.0234 0.7863 0.1904 84 R 0.0351 0.6684 0.2965 85 L 0.0763 0.3544 0.5693 86 N 0.0617 0.1522 0.7861 87 K 0.1959 0.0669 0.7372 88 K 0.2451 0.0818 0.6731 89 I 0.3321 0.0802 0.5877 90 I 0.3462 0.0512 0.6026 91 S 0.2152 0.0322 0.7527 92 W 0.0786 0.5436 0.3778 93 S 0.0594 0.6289 0.3117 94 E 0.0902 0.6368 0.2730 95 Y 0.1196 0.6125 0.2679 96 K 0.1039 0.6376 0.2585 97 N 0.1531 0.5427 0.3042 98 I 0.2089 0.3958 0.3952 99 Y 0.2479 0.2389 0.5132 100 E 0.1720 0.2671 0.5610 101 Q 0.1092 0.3370 0.5538 102 S 0.1156 0.2998 0.5846 103 I 0.1751 0.2454 0.5795 104 L 0.1863 0.1930 0.6207 105 K 0.1799 0.1385 0.6817