# This file is the result of combining several RDB files, specifically # T0210.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0210.t2k.stride-ebghtl.rdb (weight 1.24869) # T0210.t2k.str2.rdb (weight 1.54758) # T0210.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 T0210.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0210 # 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 T0210.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 47 # # ============================================ # Comments from T0210.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0210 # 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 T0210.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 47 # # ============================================ # Comments from T0210.t2k.str2.rdb # ============================================ # TARGET T0210 # 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 T0210.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 47 # # ============================================ # Comments from T0210.t2k.alpha.rdb # ============================================ # TARGET T0210 # 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 T0210.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 47 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0561 0.0437 0.9003 2 Q 0.1170 0.0821 0.8008 3 N 0.1021 0.1621 0.7358 4 A 0.0054 0.9296 0.0649 5 D 0.0049 0.9484 0.0466 6 D 0.0050 0.9536 0.0414 7 F 0.0047 0.9554 0.0399 8 I 0.0049 0.9488 0.0463 9 K 0.0053 0.9301 0.0646 10 F 0.0060 0.8659 0.1280 11 L 0.0540 0.4482 0.4978 12 E 0.0522 0.0683 0.8795 13 L 0.1133 0.0361 0.8505 14 E 0.1926 0.0229 0.7845 15 Q 0.2064 0.0332 0.7604 16 H 0.1466 0.0282 0.8252 17 V 0.0857 0.0916 0.8226 18 E 0.0572 0.0802 0.8626 19 G 0.0688 0.0789 0.8522 20 G 0.1497 0.0804 0.7699 21 F 0.3948 0.1199 0.4853 22 Y 0.5975 0.1423 0.2602 23 R 0.6087 0.1614 0.2299 24 S 0.6038 0.1400 0.2561 25 S 0.5232 0.1544 0.3224 26 Y 0.5106 0.1144 0.3750 27 R 0.3589 0.0919 0.5493 28 S 0.2020 0.0628 0.7352 29 E 0.0681 0.3039 0.6280 30 T 0.0760 0.2872 0.6367 31 A 0.1488 0.2353 0.6160 32 F 0.1320 0.1695 0.6985 33 D 0.0710 0.1358 0.7932 34 P 0.0419 0.1333 0.8248 35 S 0.0551 0.1548 0.7901 36 R 0.1096 0.1884 0.7019 37 Q 0.1167 0.2469 0.6364 38 L 0.1302 0.5506 0.3192 39 W 0.1626 0.6260 0.2114 40 S 0.3054 0.5506 0.1439 41 S 0.3849 0.5245 0.0906 42 I 0.4012 0.5317 0.0671 43 Y 0.3601 0.5647 0.0752 44 F 0.3504 0.5397 0.1099 45 L 0.3237 0.3848 0.2915 46 L 0.1923 0.1657 0.6420 47 R 0.0944 0.0643 0.8413 48 T 0.0409 0.1152 0.8439 49 G 0.0407 0.0979 0.8613 50 E 0.1103 0.0998 0.7899 51 V 0.2117 0.1068 0.6815 52 S 0.2199 0.1310 0.6491 53 H 0.1910 0.2931 0.5159 54 F 0.2430 0.2749 0.4821 55 H 0.3092 0.1999 0.4909 56 R 0.4394 0.1067 0.4539 57 L 0.3075 0.0680 0.6245 58 T 0.1699 0.0752 0.7549 59 A 0.1055 0.2991 0.5954 60 D 0.1153 0.2964 0.5883 61 E 0.4312 0.2166 0.3523 62 M 0.6613 0.1359 0.2028 63 W 0.7228 0.1579 0.1193 64 Y 0.7826 0.1116 0.1058 65 F 0.7106 0.1406 0.1488 66 H 0.5328 0.1251 0.3421 67 A 0.1409 0.0854 0.7737 68 G 0.0677 0.0355 0.8969 69 Q 0.1261 0.0195 0.8545 70 S 0.3437 0.0103 0.6460 71 L 0.8021 0.0066 0.1913 72 T 0.9096 0.0035 0.0869 73 I 0.9285 0.0030 0.0684 74 Y 0.9251 0.0037 0.0712 75 M 0.9175 0.0038 0.0788 76 I 0.8891 0.0061 0.1048 77 S 0.4519 0.0115 0.5366 78 P 0.0252 0.0997 0.8751 79 E 0.0462 0.0234 0.9304 80 G 0.0604 0.0310 0.9086 81 E 0.2289 0.0211 0.7500 82 L 0.8033 0.0074 0.1893 83 T 0.8625 0.0131 0.1243 84 T 0.9072 0.0071 0.0857 85 A 0.8904 0.0096 0.0999 86 Q 0.8695 0.0135 0.1170 87 L 0.6930 0.0421 0.2649 88 G 0.4092 0.0569 0.5339 89 L 0.2880 0.1183 0.5937 90 D 0.2437 0.1644 0.5918 91 L 0.1049 0.3672 0.5280 92 A 0.0643 0.3245 0.6112 93 A 0.0523 0.1947 0.7530 94 G 0.0476 0.0600 0.8924 95 E 0.1923 0.0388 0.7689 96 R 0.5172 0.0168 0.4660 97 P 0.5376 0.0203 0.4420 98 Q 0.7145 0.0307 0.2548 99 F 0.8526 0.0099 0.1375 100 L 0.8600 0.0084 0.1316 101 V 0.7668 0.0061 0.2272 102 P 0.3799 0.0114 0.6087 103 K 0.0417 0.1137 0.8446 104 G 0.0477 0.0975 0.8547 105 C 0.3772 0.0747 0.5481 106 I 0.7317 0.0238 0.2445 107 F 0.8234 0.0230 0.1536 108 G 0.8157 0.0241 0.1601 109 S 0.7432 0.0296 0.2272 110 A 0.7055 0.0257 0.2688 111 M 0.5830 0.0282 0.3887 112 N 0.2636 0.0278 0.7086 113 Q 0.0720 0.1040 0.8240 114 D 0.0476 0.0755 0.8768 115 G 0.2134 0.0782 0.7084 116 F 0.6711 0.0185 0.3104 117 S 0.8384 0.0102 0.1514 118 L 0.8936 0.0084 0.0980 119 V 0.8412 0.0190 0.1398 120 G 0.8008 0.0290 0.1703 121 C 0.7364 0.0530 0.2106 122 M 0.7277 0.0495 0.2228 123 V 0.5826 0.0727 0.3447 124 S 0.2427 0.0648 0.6924 125 P 0.0929 0.0930 0.8140 126 G 0.0880 0.1031 0.8089 127 F 0.3007 0.0654 0.6339 128 T 0.3865 0.0407 0.5728 129 F 0.2294 0.1717 0.5989 130 D 0.0827 0.2442 0.6732 131 D 0.0951 0.3036 0.6013 132 F 0.2485 0.2441 0.5074 133 E 0.3744 0.1690 0.4566 134 L 0.3458 0.1639 0.4903 135 F 0.2284 0.0803 0.6912 136 S 0.1122 0.0584 0.8294 137 Q 0.0169 0.7227 0.2604 138 E 0.0145 0.8138 0.1717 139 A 0.0080 0.8964 0.0956 140 L 0.0067 0.9066 0.0867 141 L 0.0063 0.8892 0.1045 142 A 0.0071 0.7916 0.2014 143 M 0.0137 0.6616 0.3248 144 Y 0.0553 0.3154 0.6292 145 P 0.0103 0.7069 0.2828 146 Q 0.0102 0.7592 0.2306 147 H 0.0080 0.8313 0.1607 148 K 0.0064 0.9380 0.0556 149 A 0.0051 0.9481 0.0468 150 V 0.0049 0.9514 0.0437 151 V 0.0051 0.9504 0.0444 152 Q 0.0053 0.9456 0.0491 153 K 0.0063 0.9104 0.0834 154 L 0.0138 0.8159 0.1703 155 S 0.0353 0.5783 0.3864 156 R 0.0392 0.4653 0.4954 157 P 0.0319 0.4757 0.4924 158 E 0.0504 0.4112 0.5384 159 V 0.0707 0.2009 0.7285 160 N 0.0459 0.0377 0.9164