# This file is the result of combining several RDB files, specifically # T0332.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0332.t2k.stride-ebghtl.rdb (weight 1.24869) # T0332.t2k.str2.rdb (weight 1.54758) # T0332.t2k.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 T0332.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0332 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0332.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1073 # # ============================================ # Comments from T0332.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0332 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0332.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1073 # # ============================================ # Comments from T0332.t2k.str2.rdb # ============================================ # TARGET T0332 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0332.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1073 # # ============================================ # Comments from T0332.t2k.alpha.rdb # ============================================ # TARGET T0332 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0332.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1073 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0651 0.1983 0.7366 2 G 0.0915 0.1097 0.7988 3 K 0.1258 0.0807 0.7935 4 S 0.1414 0.0706 0.7880 5 I 0.1135 0.0543 0.8322 6 S 0.0848 0.0338 0.8815 7 R 0.1428 0.0263 0.8310 8 L 0.7024 0.0081 0.2896 9 I 0.9005 0.0034 0.0961 10 V 0.9256 0.0032 0.0712 11 V 0.9170 0.0035 0.0795 12 A 0.8631 0.0050 0.1319 13 S 0.5306 0.0407 0.4287 14 L 0.2265 0.0247 0.7488 15 I 0.1339 0.0623 0.8038 16 D 0.0849 0.0765 0.8386 17 K 0.0748 0.0512 0.8741 18 P 0.0314 0.2445 0.7241 19 T 0.0338 0.3329 0.6333 20 N 0.0533 0.5689 0.3777 21 L 0.0105 0.8837 0.1058 22 G 0.0065 0.9408 0.0527 23 G 0.0056 0.9534 0.0410 24 L 0.0053 0.9581 0.0366 25 C 0.0050 0.9589 0.0361 26 R 0.0053 0.9557 0.0390 27 T 0.0050 0.9524 0.0426 28 C 0.0047 0.9504 0.0448 29 E 0.0057 0.9338 0.0605 30 V 0.0068 0.8493 0.1439 31 F 0.0415 0.3871 0.5714 32 G 0.0591 0.0314 0.9095 33 A 0.1068 0.0107 0.8825 34 S 0.2195 0.0398 0.7407 35 V 0.8732 0.0063 0.1205 36 L 0.9228 0.0035 0.0737 37 V 0.9209 0.0039 0.0753 38 V 0.8724 0.0055 0.1221 39 G 0.4926 0.0245 0.4830 40 S 0.1178 0.0465 0.8358 41 L 0.0421 0.1446 0.8133 42 Q 0.0640 0.1513 0.7847 43 C 0.1141 0.1225 0.7635 44 I 0.1056 0.1155 0.7789 45 S 0.0626 0.1857 0.7516 46 D 0.0593 0.1739 0.7668 47 K 0.0665 0.1935 0.7400 48 Q 0.0097 0.8667 0.1236 49 F 0.0111 0.8954 0.0934 50 Q 0.0185 0.9088 0.0727 51 H 0.0323 0.8889 0.0788 52 L 0.0363 0.8698 0.0938 53 S 0.0339 0.8390 0.1272 54 V 0.0461 0.7466 0.2073 55 S 0.0734 0.5662 0.3604 56 A 0.0421 0.4374 0.5204 57 E 0.0496 0.2206 0.7298 58 Q 0.1291 0.2433 0.6276 59 W 0.2556 0.2238 0.5207 60 L 0.3377 0.2198 0.4425 61 P 0.4791 0.1354 0.3856 62 L 0.5123 0.0365 0.4512 63 V 0.5533 0.0220 0.4247 64 E 0.7447 0.0241 0.2313 65 V 0.7795 0.0240 0.1965 66 K 0.7746 0.0153 0.2101 67 P 0.5035 0.0158 0.4807 68 P 0.1458 0.0696 0.7846 69 Q 0.1099 0.0186 0.8715 70 L 0.0071 0.8958 0.0971 71 I 0.0049 0.9480 0.0471 72 D 0.0049 0.9533 0.0419 73 Y 0.0049 0.9539 0.0413 74 L 0.0050 0.9486 0.0465 75 Q 0.0050 0.9256 0.0693 76 Q 0.0055 0.9174 0.0771 77 K 0.0095 0.8971 0.0934 78 K 0.0062 0.8692 0.1246 79 T 0.0086 0.7646 0.2268 80 E 0.0468 0.2502 0.7031 81 G 0.0436 0.0205 0.9359 82 Y 0.2080 0.0075 0.7845 83 T 0.8052 0.0044 0.1904 84 I 0.9135 0.0033 0.0832 85 I 0.9136 0.0050 0.0813 86 G 0.8986 0.0046 0.0968 87 V 0.8155 0.0102 0.1743 88 E 0.5380 0.0121 0.4500 89 Q 0.2238 0.0567 0.7195 90 T 0.1114 0.0815 0.8071 91 A 0.0647 0.1734 0.7619 92 K 0.0616 0.1410 0.7974 93 S 0.1961 0.0962 0.7078 94 L 0.3413 0.0616 0.5970 95 D 0.3902 0.0757 0.5341 96 L 0.1973 0.4202 0.3825 97 T 0.1474 0.4977 0.3548 98 Q 0.1769 0.4345 0.3886 99 Y 0.2371 0.2045 0.5583 100 C 0.1847 0.1103 0.7049 101 F 0.1258 0.0988 0.7755 102 P 0.0797 0.0872 0.8331 103 E 0.0799 0.0434 0.8768 104 K 0.1501 0.0407 0.8092 105 S 0.8341 0.0048 0.1611 106 L 0.9274 0.0033 0.0693 107 L 0.9286 0.0034 0.0681 108 L 0.9174 0.0034 0.0792 109 L 0.7214 0.0206 0.2580 110 G 0.2604 0.0205 0.7191 111 N 0.1451 0.0762 0.7787 112 E 0.0830 0.1940 0.7230 113 R 0.0607 0.2218 0.7175 114 E 0.0439 0.1497 0.8064 115 G 0.0555 0.0799 0.8646 116 I 0.0999 0.0341 0.8660 117 P 0.0528 0.0272 0.9201 118 A 0.0059 0.9173 0.0769 119 N 0.0049 0.9340 0.0611 120 L 0.0055 0.9370 0.0575 121 I 0.0055 0.9350 0.0595 122 Q 0.0081 0.8426 0.1493 123 Q 0.0174 0.5812 0.4015 124 L 0.0733 0.2288 0.6978 125 D 0.0658 0.1284 0.8058 126 V 0.4146 0.0959 0.4895 127 C 0.7686 0.0290 0.2024 128 V 0.8723 0.0099 0.1179 129 E 0.8815 0.0072 0.1113 130 I 0.7114 0.0065 0.2821 131 P 0.3407 0.0164 0.6428 132 Q 0.1367 0.0460 0.8174 133 Q 0.0938 0.0638 0.8424 134 G 0.0573 0.0767 0.8660 135 I 0.0985 0.1470 0.7545 136 I 0.2659 0.1884 0.5458 137 R 0.2682 0.2426 0.4892 138 S 0.2684 0.3210 0.4106 139 L 0.0843 0.7220 0.1937 140 N 0.0317 0.8571 0.1112 141 V 0.0078 0.9370 0.0552 142 H 0.0055 0.9537 0.0407 143 V 0.0047 0.9572 0.0381 144 S 0.0047 0.9598 0.0356 145 G 0.0047 0.9602 0.0351 146 A 0.0047 0.9604 0.0349 147 L 0.0047 0.9607 0.0347 148 L 0.0047 0.9611 0.0342 149 I 0.0047 0.9607 0.0346 150 W 0.0047 0.9599 0.0354 151 E 0.0047 0.9586 0.0367 152 Y 0.0053 0.9535 0.0412 153 T 0.0063 0.9398 0.0538 154 R 0.0073 0.8856 0.1071 155 Q 0.0094 0.8166 0.1740 156 Q 0.0414 0.5702 0.3884 157 L 0.0496 0.2288 0.7216 158 L 0.0576 0.0526 0.8898 159 S 0.0403 0.0400 0.9197