# This file is the result of combining several RDB files, specifically # T0370.t06.dssp-ebghstl.rdb (weight 1.53986) # T0370.t06.stride-ebghtl.rdb (weight 1.24869) # T0370.t06.str2.rdb (weight 1.54758) # T0370.t06.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 T0370.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 692 # # ============================================ # Comments from T0370.t06.stride-ebghtl.rdb # ============================================ # TARGET T0370 # Using neural net t06-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 T0370.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 692 # # ============================================ # Comments from T0370.t06.str2.rdb # ============================================ # TARGET T0370 # 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 T0370.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 692 # # ============================================ # Comments from T0370.t06.alpha.rdb # ============================================ # TARGET T0370 # Using neural net 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 T0370.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 692 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0564 0.0206 0.9229 2 T 0.0605 0.0418 0.8977 3 T 0.0538 0.0834 0.8628 4 P 0.0705 0.1054 0.8241 5 P 0.0291 0.5035 0.4674 6 A 0.0178 0.7537 0.2286 7 R 0.0125 0.8669 0.1205 8 T 0.0149 0.8829 0.1022 9 A 0.0120 0.8845 0.1035 10 K 0.0094 0.8939 0.0967 11 Q 0.0104 0.8719 0.1178 12 R 0.0097 0.8596 0.1307 13 I 0.0056 0.9208 0.0736 14 Q 0.0050 0.9479 0.0470 15 D 0.0051 0.9464 0.0486 16 T 0.0049 0.9429 0.0522 17 L 0.0053 0.9322 0.0625 18 N 0.0065 0.8625 0.1310 19 R 0.0084 0.7659 0.2257 20 L 0.0440 0.5427 0.4133 21 E 0.0540 0.2806 0.6654 22 L 0.0777 0.1884 0.7339 23 D 0.1083 0.0518 0.8399 24 V 0.1116 0.0444 0.8440 25 D 0.2137 0.0373 0.7491 26 A 0.7458 0.0085 0.2457 27 W 0.8993 0.0046 0.0961 28 V 0.9177 0.0042 0.0781 29 S 0.9025 0.0052 0.0923 30 T 0.8275 0.0064 0.1661 31 A 0.6866 0.0174 0.2960 32 G 0.3369 0.0150 0.6481 33 A 0.0503 0.1035 0.8462 34 D 0.0405 0.0676 0.8920 35 G 0.0529 0.0673 0.8798 36 G 0.0650 0.0341 0.9009 37 A 0.2281 0.0200 0.7519 38 P 0.4844 0.0234 0.4922 39 Y 0.6812 0.0177 0.3010 40 L 0.8029 0.0079 0.1892 41 V 0.7950 0.0078 0.1972 42 P 0.8326 0.0054 0.1619 43 L 0.8118 0.0122 0.1761 44 S 0.8418 0.0083 0.1499 45 Y 0.8523 0.0076 0.1401 46 L 0.8647 0.0066 0.1287 47 W 0.8195 0.0136 0.1669 48 D 0.4408 0.0214 0.5378 49 G 0.0518 0.0507 0.8974 50 E 0.1149 0.0668 0.8183 51 T 0.8046 0.0083 0.1872 52 F 0.9146 0.0035 0.0819 53 L 0.9286 0.0034 0.0680 54 V 0.9189 0.0041 0.0769 55 A 0.8591 0.0075 0.1334 56 T 0.4306 0.0090 0.5603 57 P 0.0935 0.0911 0.8155 58 A 0.0196 0.1388 0.8415 59 A 0.0241 0.1068 0.8692 60 S 0.0589 0.0581 0.8830 61 P 0.0359 0.4566 0.5075 62 T 0.0792 0.5854 0.3354 63 G 0.0514 0.7509 0.1977 64 R 0.0424 0.8106 0.1470 65 N 0.0791 0.7671 0.1537 66 L 0.0355 0.8268 0.1377 67 S 0.0390 0.7259 0.2350 68 E 0.0573 0.4876 0.4550 69 T 0.1002 0.0544 0.8454 70 G 0.0956 0.0846 0.8198 71 R 0.3572 0.0451 0.5978 72 V 0.7945 0.0121 0.1934 73 R 0.8939 0.0072 0.0990 74 L 0.9136 0.0043 0.0821 75 G 0.8956 0.0053 0.0992 76 I 0.8131 0.0103 0.1766 77 G 0.4073 0.0113 0.5814 78 P 0.2041 0.0471 0.7488 79 T 0.1021 0.1176 0.7803 80 R 0.0791 0.1301 0.7908 81 D 0.1567 0.0793 0.7640 82 L 0.7336 0.0101 0.2564 83 V 0.9021 0.0038 0.0940 84 L 0.9287 0.0032 0.0681 85 V 0.9201 0.0039 0.0760 86 E 0.8612 0.0200 0.1188 87 G 0.8473 0.0062 0.1465 88 T 0.8631 0.0048 0.1322 89 A 0.8628 0.0045 0.1327 90 L 0.8486 0.0065 0.1448 91 P 0.8203 0.0047 0.1750 92 L 0.3673 0.0219 0.6108 93 E 0.1727 0.0138 0.8135 94 P 0.0378 0.2910 0.6711 95 A 0.0178 0.3130 0.6692 96 G 0.0274 0.2785 0.6942 97 L 0.0590 0.0996 0.8414 98 P 0.0690 0.3219 0.6091 99 D 0.0391 0.5364 0.4245 100 G 0.0506 0.5671 0.3823 101 V 0.0511 0.6650 0.2839 102 G 0.0420 0.7400 0.2180 103 D 0.0219 0.8132 0.1649 104 T 0.0167 0.8633 0.1200 105 F 0.0139 0.8795 0.1066 106 A 0.0160 0.8593 0.1247 107 E 0.0189 0.7850 0.1961 108 K 0.0344 0.6176 0.3480 109 T 0.0590 0.3053 0.6357 110 G 0.0466 0.1003 0.8530 111 F 0.0687 0.0529 0.8784 112 D 0.0959 0.0391 0.8650 113 P 0.0866 0.1577 0.7557 114 R 0.1720 0.1379 0.6901 115 R 0.2324 0.0916 0.6760 116 L 0.1951 0.0510 0.7540 117 T 0.1731 0.0424 0.7845 118 T 0.0790 0.1007 0.8203 119 S 0.1650 0.0569 0.7781 120 Y 0.6464 0.0152 0.3383 121 L 0.8622 0.0051 0.1327 122 Y 0.9225 0.0035 0.0740 123 F 0.9184 0.0038 0.0777 124 R 0.9220 0.0035 0.0746 125 I 0.9015 0.0039 0.0946 126 S 0.7807 0.0058 0.2136 127 P 0.6676 0.0143 0.3181 128 R 0.5981 0.0570 0.3449 129 R 0.8720 0.0174 0.1107 130 V 0.8936 0.0138 0.0926 131 Q 0.8867 0.0201 0.0932 132 A 0.8395 0.0298 0.1307 133 W 0.7212 0.0479 0.2309 134 R 0.4816 0.0758 0.4426 135 E 0.2471 0.1522 0.6007 136 A 0.1167 0.1457 0.7377 137 N 0.0928 0.1041 0.8031 138 E 0.1589 0.0985 0.7426 139 L 0.2859 0.1187 0.5953 140 S 0.3046 0.1031 0.5923 141 G 0.2707 0.1257 0.6035 142 R 0.5141 0.0963 0.3896 143 E 0.6854 0.0784 0.2362 144 L 0.7846 0.0588 0.1567 145 M 0.7545 0.0490 0.1965 146 R 0.5815 0.0633 0.3553 147 D 0.0733 0.0398 0.8869 148 G 0.0331 0.0381 0.9289 149 E 0.4370 0.0233 0.5397 150 W 0.7850 0.0086 0.2064 151 L 0.7856 0.0126 0.2018 152 V 0.6432 0.0187 0.3381 153 T 0.2703 0.0162 0.7135 154 D 0.0822 0.0258 0.8920