# This file is the result of combining several RDB files, specifically # T0307.t04.dssp-ebghstl.rdb (weight 1.53986) # T0307.t04.stride-ebghtl.rdb (weight 1.24869) # T0307.t04.str2.rdb (weight 1.54758) # T0307.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 T0307.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 T0307.t04.stride-ebghtl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 T0307.t04.str2.rdb # ============================================ # TARGET T0307 # 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 T0307.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 T0307.t04.alpha.rdb # ============================================ # TARGET T0307 # 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 T0307.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 0.1040 0.1160 0.7800 2 G 0.1157 0.1298 0.7546 3 L 0.1218 0.1633 0.7150 4 G 0.1318 0.1219 0.7463 5 R 0.1699 0.2094 0.6207 6 Q 0.2571 0.1432 0.5997 7 S 0.4215 0.1107 0.4678 8 L 0.5065 0.0769 0.4166 9 N 0.5929 0.0607 0.3464 10 I 0.7146 0.0742 0.2112 11 M 0.7736 0.0501 0.1763 12 T 0.7016 0.0554 0.2430 13 F 0.4709 0.0877 0.4415 14 S 0.1735 0.1013 0.7252 15 G 0.0546 0.2225 0.7229 16 Q 0.0950 0.5599 0.3451 17 E 0.1628 0.6450 0.1923 18 L 0.0750 0.8201 0.1049 19 T 0.0559 0.8768 0.0673 20 A 0.0648 0.8855 0.0497 21 I 0.0579 0.8962 0.0458 22 I 0.0707 0.8791 0.0501 23 K 0.0764 0.8598 0.0638 24 M 0.0663 0.8223 0.1114 25 A 0.0695 0.7598 0.1708 26 K 0.0869 0.6880 0.2251 27 S 0.1697 0.6045 0.2258 28 M 0.2650 0.5247 0.2103 29 V 0.4260 0.3573 0.2166 30 M 0.4023 0.2778 0.3200 31 A 0.2655 0.2428 0.4917 32 D 0.0791 0.0882 0.8327 33 G 0.0679 0.0451 0.8870 34 K 0.2429 0.0275 0.7296 35 I 0.4094 0.0123 0.5783 36 K 0.2044 0.0128 0.7828 37 P 0.2166 0.2380 0.5454 38 A 0.1806 0.4491 0.3703 39 E 0.2532 0.5053 0.2414 40 I 0.4043 0.4256 0.1700 41 A 0.5005 0.3620 0.1375 42 V 0.4914 0.3675 0.1411 43 M 0.4710 0.2979 0.2311 44 T 0.2991 0.3572 0.3437 45 R 0.0623 0.7673 0.1705 46 E 0.0614 0.8098 0.1288 47 F 0.0619 0.8272 0.1109 48 M 0.0907 0.7779 0.1314 49 R 0.0949 0.7608 0.1442 50 F 0.0754 0.6956 0.2290 51 G 0.0875 0.4966 0.4159 52 I 0.1627 0.4659 0.3714 53 L 0.1710 0.4964 0.3325 54 Q 0.0825 0.6194 0.2981 55 D 0.0663 0.6187 0.3150 56 Q 0.0595 0.7511 0.1894 57 V 0.1030 0.7471 0.1499 58 D 0.1278 0.7342 0.1379 59 L 0.1647 0.7378 0.0974 60 L 0.1819 0.7210 0.0971 61 L 0.2142 0.6355 0.1504 62 K 0.1743 0.5414 0.2843 63 A 0.0792 0.4643 0.4565 64 S 0.0594 0.3709 0.5697 65 D 0.0414 0.3139 0.6448 66 S 0.0865 0.4313 0.4822 67 I 0.1360 0.5155 0.3484 68 E 0.1337 0.4963 0.3700 69 A 0.0664 0.7064 0.2272 70 S 0.0518 0.7647 0.1836 71 Q 0.0669 0.7920 0.1412 72 A 0.0859 0.8191 0.0950 73 V 0.1296 0.7981 0.0722 74 A 0.1279 0.8093 0.0628 75 L 0.0912 0.8439 0.0649 76 I 0.0941 0.8153 0.0905 77 A 0.1204 0.7134 0.1663 78 R 0.1056 0.5731 0.3213 79 M 0.0846 0.3568 0.5585 80 D 0.0611 0.3244 0.6145 81 E 0.0051 0.9169 0.0780 82 E 0.0062 0.9170 0.0768 83 R 0.0076 0.9169 0.0755 84 K 0.0085 0.9274 0.0642 85 K 0.0113 0.9157 0.0730 86 Y 0.0176 0.9032 0.0792 87 V 0.0286 0.8873 0.0842 88 A 0.0410 0.8544 0.1046 89 S 0.0609 0.7744 0.1647 90 Y 0.1090 0.6678 0.2232 91 L 0.2064 0.4842 0.3094 92 G 0.3706 0.2752 0.3542 93 V 0.6153 0.2005 0.1842 94 I 0.7516 0.1182 0.1302 95 M 0.7424 0.0748 0.1829 96 A 0.5185 0.0598 0.4217 97 S 0.2415 0.0866 0.6719 98 D 0.1028 0.0720 0.8251 99 G 0.0940 0.0523 0.8537 100 D 0.2055 0.0397 0.7548 101 I 0.2365 0.0726 0.6909 102 D 0.1110 0.0765 0.8125 103 D 0.0288 0.4161 0.5551 104 N 0.0254 0.4952 0.4794 105 E 0.0472 0.7337 0.2191 106 L 0.0681 0.8054 0.1265 107 A 0.0854 0.8176 0.0970 108 L 0.0668 0.8661 0.0671 109 W 0.0698 0.8655 0.0647 110 T 0.0785 0.8621 0.0595 111 L 0.0446 0.8905 0.0648 112 I 0.0340 0.8945 0.0715 113 S 0.0260 0.8817 0.0923 114 T 0.0190 0.8551 0.1259 115 L 0.0325 0.7180 0.2495 116 C 0.0570 0.3975 0.5455 117 G 0.0419 0.1589 0.7993 118 L 0.0691 0.0956 0.8353 119 P 0.0848 0.1727 0.7425 120 T 0.1313 0.4111 0.4576 121 M 0.1718 0.5997 0.2286 122 T 0.1797 0.6752 0.1451 123 V 0.0822 0.8385 0.0793 124 M 0.0523 0.8782 0.0695 125 E 0.0526 0.8763 0.0711 126 A 0.0372 0.8849 0.0780 127 I 0.0294 0.8611 0.1096 128 N 0.0253 0.7683 0.2064 129 N 0.0270 0.6135 0.3596 130 M 0.0493 0.4645 0.4862 131 K 0.0417 0.3595 0.5988 132 N 0.0603 0.1795 0.7602 133 L 0.0389 0.0612 0.8999