# This file is the result of combining several RDB files, specifically # T0274.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0274.t2k.stride-ebghtl.rdb (weight 1.24869) # T0274.t2k.str2.rdb (weight 1.54758) # T0274.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 T0274.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0274 # 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 T0274.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 250 # # ============================================ # Comments from T0274.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0274 # 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 T0274.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 250 # # ============================================ # Comments from T0274.t2k.str2.rdb # ============================================ # TARGET T0274 # 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 T0274.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 250 # # ============================================ # Comments from T0274.t2k.alpha.rdb # ============================================ # TARGET T0274 # 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 T0274.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 250 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0740 0.0292 0.8969 2 N 0.0978 0.0360 0.8663 3 L 0.0059 0.9018 0.0923 4 E 0.0052 0.9285 0.0663 5 A 0.0053 0.9352 0.0595 6 K 0.0055 0.9415 0.0530 7 K 0.0050 0.9440 0.0509 8 K 0.0055 0.9297 0.0648 9 V 0.0056 0.9104 0.0840 10 L 0.0105 0.8529 0.1367 11 R 0.0085 0.6764 0.3151 12 S 0.0214 0.5247 0.4539 13 F 0.0852 0.2128 0.7020 14 T 0.0730 0.0852 0.8419 15 Y 0.1261 0.0619 0.8120 16 G 0.4049 0.0306 0.5645 17 L 0.8537 0.0046 0.1418 18 Y 0.9161 0.0035 0.0805 19 V 0.9272 0.0031 0.0697 20 L 0.9167 0.0046 0.0787 21 T 0.8908 0.0053 0.1039 22 A 0.7767 0.0123 0.2110 23 K 0.4446 0.0332 0.5222 24 D 0.1511 0.0459 0.8030 25 G 0.0394 0.0579 0.9027 26 D 0.0516 0.0539 0.8945 27 E 0.3636 0.0234 0.6131 28 V 0.6353 0.0200 0.3447 29 A 0.6980 0.0295 0.2725 30 A 0.7894 0.0192 0.1914 31 G 0.8297 0.0145 0.1558 32 T 0.8220 0.0181 0.1598 33 V 0.7885 0.0429 0.1687 34 N 0.7154 0.0603 0.2243 35 W 0.6895 0.0784 0.2321 36 V 0.6889 0.0581 0.2530 37 T 0.6522 0.0589 0.2888 38 Q 0.6966 0.0564 0.2470 39 A 0.6280 0.0782 0.2938 40 S 0.5495 0.0649 0.3856 41 F 0.3445 0.0733 0.5822 42 Q 0.1449 0.0331 0.8220 43 P 0.1132 0.0222 0.8646 44 P 0.2499 0.0166 0.7335 45 L 0.7791 0.0068 0.2142 46 V 0.9112 0.0035 0.0853 47 A 0.9248 0.0034 0.0718 48 V 0.9184 0.0040 0.0776 49 G 0.8836 0.0041 0.1123 50 L 0.6858 0.0187 0.2955 51 K 0.3120 0.0256 0.6624 52 R 0.0540 0.1583 0.7877 53 D 0.0404 0.2030 0.7567 54 S 0.0560 0.3506 0.5934 55 H 0.0662 0.4671 0.4668 56 L 0.0816 0.5569 0.3615 57 H 0.0280 0.8155 0.1565 58 A 0.0281 0.8780 0.0939 59 L 0.0275 0.8871 0.0854 60 V 0.0470 0.8693 0.0837 61 E 0.0408 0.8381 0.1211 62 R 0.0346 0.7166 0.2488 63 T 0.0558 0.1979 0.7463 64 G 0.0278 0.0536 0.9186 65 K 0.3906 0.0223 0.5871 66 L 0.8380 0.0056 0.1564 67 A 0.8979 0.0060 0.0961 68 L 0.9012 0.0066 0.0923 69 M 0.8389 0.0104 0.1507 70 T 0.5569 0.0243 0.4188 71 L 0.2245 0.0248 0.7507 72 A 0.0899 0.0664 0.8437 73 H 0.0108 0.6619 0.3273 74 D 0.0085 0.7562 0.2353 75 Q 0.0055 0.8963 0.0982 76 K 0.0056 0.9371 0.0573 77 A 0.0058 0.9448 0.0494 78 I 0.0049 0.9484 0.0467 79 A 0.0051 0.9460 0.0490 80 Q 0.0052 0.9364 0.0584 81 D 0.0075 0.9055 0.0870 82 F 0.0154 0.8068 0.1778 83 F 0.0331 0.6096 0.3572 84 K 0.0427 0.4549 0.5024 85 P 0.0416 0.3541 0.6043 86 T 0.0592 0.2054 0.7354 87 V 0.0498 0.1470 0.8032 88 R 0.0588 0.1941 0.7471 89 E 0.0636 0.3105 0.6258 90 G 0.0594 0.4216 0.5190 91 D 0.1018 0.4267 0.4715 92 R 0.1198 0.4560 0.4241 93 L 0.1434 0.3630 0.4936 94 N 0.0916 0.2527 0.6558 95 G 0.1040 0.0873 0.8087 96 H 0.2113 0.0340 0.7547 97 P 0.3788 0.0244 0.5968 98 F 0.5456 0.0421 0.4122 99 E 0.5062 0.0389 0.4549 100 P 0.4218 0.0696 0.5086 101 S 0.2551 0.0947 0.6502 102 P 0.0943 0.2005 0.7051 103 T 0.0765 0.1752 0.7483 104 F 0.0954 0.1135 0.7911 105 G 0.0763 0.0550 0.8687 106 L 0.1819 0.0251 0.7930 107 P 0.3417 0.0518 0.6064 108 L 0.4647 0.0987 0.4366 109 L 0.3609 0.1889 0.4503 110 T 0.1837 0.2623 0.5540 111 E 0.1557 0.1454 0.6989 112 L 0.3044 0.0437 0.6518 113 P 0.5567 0.0277 0.4156 114 Y 0.8225 0.0200 0.1575 115 W 0.9104 0.0074 0.0822 116 L 0.9144 0.0056 0.0799 117 E 0.9180 0.0047 0.0773 118 A 0.8872 0.0043 0.1086 119 E 0.8595 0.0069 0.1336 120 V 0.8579 0.0059 0.1362 121 R 0.7744 0.0231 0.2025 122 H 0.7841 0.0125 0.2034 123 L 0.7433 0.0210 0.2357 124 Y 0.6852 0.0166 0.2981 125 P 0.5483 0.0293 0.4224 126 G 0.2917 0.0459 0.6624 127 G 0.2012 0.0449 0.7539 128 D 0.2580 0.0462 0.6958 129 H 0.6113 0.0181 0.3705 130 S 0.8481 0.0068 0.1452 131 L 0.9158 0.0038 0.0805 132 V 0.9258 0.0036 0.0706 133 V 0.9104 0.0052 0.0843 134 A 0.8830 0.0058 0.1112 135 E 0.8878 0.0053 0.1069 136 V 0.8989 0.0032 0.0978 137 V 0.8502 0.0181 0.1317 138 E 0.8587 0.0066 0.1347 139 A 0.8400 0.0113 0.1486 140 G 0.8505 0.0085 0.1410 141 V 0.7324 0.0158 0.2518 142 R 0.3186 0.0308 0.6506 143 R 0.0818 0.0917 0.8265 144 E 0.0484 0.0851 0.8665 145 E 0.1147 0.0570 0.8284 146 K 0.1720 0.0311 0.7968 147 P 0.4572 0.0299 0.5129 148 L 0.8117 0.0216 0.1667 149 V 0.8895 0.0127 0.0978 150 M 0.8856 0.0142 0.1002 151 W 0.8014 0.0310 0.1677 152 D 0.4241 0.0588 0.5172 153 T 0.1539 0.0750 0.7711 154 G 0.3613 0.0828 0.5558 155 W 0.6679 0.0516 0.2805 156 F 0.6949 0.0416 0.2635 157 Y 0.5853 0.0494 0.3653 158 G 0.2472 0.0587 0.6941 159 G 0.0515 0.0339 0.9146