# This file is the result of combining several RDB files, specifically # T0314.t04.dssp-ebghstl.rdb (weight 1.53986) # T0314.t04.stride-ebghtl.rdb (weight 1.24869) # T0314.t04.str2.rdb (weight 1.54758) # T0314.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 T0314.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.stride-ebghtl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.str2.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.alpha.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1103 0.0142 0.8755 2 S 0.3514 0.0218 0.6268 3 I 0.3562 0.0283 0.6155 4 T 0.2045 0.0375 0.7579 5 S 0.0495 0.6085 0.3420 6 T 0.0054 0.9311 0.0635 7 D 0.0057 0.9400 0.0543 8 I 0.0050 0.9429 0.0521 9 C 0.0052 0.9412 0.0535 10 Q 0.0053 0.9216 0.0731 11 A 0.0067 0.8854 0.1078 12 A 0.0093 0.8628 0.1279 13 D 0.0117 0.7623 0.2260 14 A 0.0143 0.7010 0.2847 15 L 0.0663 0.5192 0.4145 16 K 0.0601 0.3377 0.6022 17 G 0.1460 0.2102 0.6439 18 F 0.3797 0.1733 0.4470 19 V 0.5352 0.1206 0.3442 20 G 0.5072 0.0735 0.4193 21 F 0.4627 0.0798 0.4575 22 N 0.4173 0.0634 0.5193 23 R 0.1542 0.1373 0.7085 24 K 0.1624 0.1486 0.6890 25 T 0.1340 0.0554 0.8105 26 G 0.2234 0.0246 0.7520 27 R 0.5754 0.0095 0.4151 28 Y 0.9009 0.0036 0.0955 29 I 0.9189 0.0034 0.0777 30 V 0.9227 0.0033 0.0740 31 R 0.8969 0.0041 0.0989 32 F 0.6866 0.0126 0.3008 33 S 0.3763 0.0203 0.6033 34 E 0.1120 0.1616 0.7264 35 D 0.0621 0.2203 0.7176 36 S 0.0670 0.3199 0.6131 37 F 0.1115 0.1547 0.7338 38 G 0.1430 0.1136 0.7434 39 M 0.2235 0.0840 0.6925 40 D 0.2952 0.0890 0.6158 41 V 0.1501 0.2822 0.5677 42 A 0.1299 0.2529 0.6171 43 D 0.1214 0.2379 0.6407 44 D 0.0545 0.2357 0.7098 45 S 0.0889 0.1510 0.7600 46 I 0.2482 0.0697 0.6822 47 T 0.2342 0.0251 0.7407 48 P 0.2272 0.0320 0.7408 49 T 0.1616 0.1611 0.6774 50 S 0.1809 0.2390 0.5801 51 E 0.3313 0.2604 0.4083 52 F 0.5802 0.1131 0.3067 53 V 0.7078 0.0663 0.2260 54 W 0.7001 0.0551 0.2448 55 S 0.5250 0.0556 0.4194 56 S 0.3432 0.1260 0.5308 57 V 0.1973 0.1752 0.6275 58 R 0.1618 0.1457 0.6925 59 D 0.0916 0.2003 0.7081 60 D 0.1729 0.2427 0.5844 61 V 0.4634 0.2251 0.3115 62 M 0.5698 0.1561 0.2741 63 R 0.5178 0.1922 0.2899 64 L 0.3050 0.2812 0.4138 65 G 0.1550 0.2657 0.5793 66 R 0.0347 0.7969 0.1684 67 E 0.0314 0.8886 0.0800 68 Q 0.0217 0.9247 0.0536 69 L 0.0193 0.9325 0.0482 70 Q 0.0153 0.9395 0.0452 71 I 0.0135 0.9441 0.0424 72 L 0.0168 0.9283 0.0549 73 L 0.0205 0.8856 0.0939 74 E 0.0247 0.7882 0.1870 75 Q 0.0644 0.5176 0.4181 76 N 0.0755 0.2278 0.6968 77 I 0.0609 0.3736 0.5656 78 N 0.0560 0.3700 0.5740 79 E 0.0678 0.4815 0.4508 80 R 0.1614 0.4024 0.4362 81 L 0.3003 0.2522 0.4476 82 N 0.2621 0.1088 0.6291 83 I 0.0979 0.1390 0.7631 84 G 0.0557 0.1088 0.8354 85 E 0.1086 0.0897 0.8018 86 P 0.2352 0.1590 0.6058 87 L 0.4589 0.1770 0.3641 88 L 0.7180 0.1221 0.1599 89 V 0.7843 0.1004 0.1153 90 Y 0.7880 0.0896 0.1224 91 L 0.7072 0.0886 0.2041 92 R 0.4969 0.0882 0.4149 93 R 0.1555 0.3216 0.5229 94 Q 0.0638 0.2907 0.6455 95 D 0.0549 0.2179 0.7272 96 L 0.0914 0.0843 0.8243 97 P 0.0797 0.1931 0.7273 98 E 0.2943 0.3649 0.3408 99 I 0.4792 0.3195 0.2013 100 T 0.5880 0.2453 0.1667 101 A 0.5780 0.2481 0.1739 102 Q 0.5211 0.2728 0.2061 103 R 0.4572 0.2392 0.3036 104 Q 0.2962 0.2406 0.4632 105 L 0.1406 0.1544 0.7050 106 R 0.0435 0.0654 0.8911