# This file is the result of combining several RDB files, specifically # T0255.t04.dssp-ebghstl.rdb (weight 1.53986) # T0255.t04.stride-ebghtl.rdb (weight 1.24869) # T0255.t04.str2.rdb (weight 1.54758) # T0255.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 T0255.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0255 # Using neural net t04-2621-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 T0255.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 95.2774 # # ============================================ # Comments from T0255.t04.stride-ebghtl.rdb # ============================================ # TARGET T0255 # 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 T0255.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 95.2774 # # ============================================ # Comments from T0255.t04.str2.rdb # ============================================ # TARGET T0255 # Using neural net t04-2621-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 T0255.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 95.2774 # # ============================================ # Comments from T0255.t04.alpha.rdb # ============================================ # TARGET T0255 # 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 T0255.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 95.2774 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0717 0.0621 0.8662 2 N 0.0923 0.0708 0.8368 3 S 0.0714 0.1668 0.7619 4 K 0.0935 0.1238 0.7827 5 N 0.3142 0.0432 0.6426 6 T 0.5184 0.0148 0.4668 7 I 0.7078 0.0214 0.2708 8 C 0.8356 0.0264 0.1380 9 L 0.8619 0.0239 0.1142 10 W 0.8002 0.0252 0.1747 11 Y 0.5393 0.0477 0.4130 12 D 0.1877 0.0588 0.7535 13 S 0.0165 0.5149 0.4686 14 A 0.0183 0.7086 0.2731 15 A 0.0050 0.9372 0.0578 16 L 0.0048 0.9569 0.0384 17 E 0.0048 0.9560 0.0392 18 A 0.0048 0.9566 0.0386 19 A 0.0047 0.9576 0.0377 20 T 0.0047 0.9551 0.0402 21 F 0.0047 0.9526 0.0427 22 Y 0.0048 0.9464 0.0487 23 A 0.0050 0.9352 0.0598 24 E 0.0065 0.8836 0.1099 25 T 0.0124 0.7366 0.2510 26 F 0.0652 0.1227 0.8122 27 P 0.0445 0.0840 0.8715 28 D 0.0525 0.2863 0.6611 29 S 0.0795 0.3887 0.5318 30 A 0.3025 0.3516 0.3459 31 V 0.6270 0.1842 0.1888 32 L 0.7364 0.1124 0.1513 33 A 0.7739 0.0917 0.1344 34 V 0.7261 0.0966 0.1773 35 H 0.6148 0.0839 0.3014 36 R 0.3705 0.0745 0.5550 37 A 0.1576 0.0314 0.8110 38 P 0.0769 0.0805 0.8426 39 G 0.0561 0.0806 0.8633 40 D 0.0770 0.0805 0.8425 41 Y 0.0966 0.0357 0.8677 42 P 0.0922 0.0497 0.8582 43 S 0.0978 0.1040 0.7982 44 G 0.0629 0.0965 0.8406 45 K 0.0962 0.1130 0.7909 46 E 0.0839 0.1112 0.8049 47 G 0.0960 0.0518 0.8521 48 D 0.3154 0.0229 0.6617 49 V 0.8312 0.0046 0.1642 50 L 0.8847 0.0058 0.1095 51 T 0.9230 0.0034 0.0736 52 V 0.9173 0.0036 0.0790 53 E 0.9261 0.0033 0.0707 54 F 0.9241 0.0036 0.0723 55 R 0.9050 0.0037 0.0912 56 V 0.7614 0.0198 0.2188 57 M 0.1105 0.0294 0.8601 58 G 0.0620 0.0326 0.9054 59 I 0.5973 0.0132 0.3895 60 P 0.7926 0.0089 0.1985 61 C 0.8623 0.0153 0.1223 62 L 0.8571 0.0183 0.1246 63 G 0.7810 0.0300 0.1890 64 L 0.6115 0.0448 0.3437 65 N 0.2921 0.0366 0.6713 66 G 0.1211 0.0507 0.8282 67 G 0.0806 0.0647 0.8548 68 P 0.0781 0.2356 0.6863 69 A 0.0750 0.2967 0.6283 70 F 0.1132 0.1855 0.7012 71 R 0.1262 0.1117 0.7621 72 H 0.1041 0.1007 0.7952 73 S 0.0977 0.0747 0.8275 74 E 0.1064 0.0897 0.8040 75 A 0.2747 0.0369 0.6883 76 F 0.7446 0.0079 0.2475 77 S 0.8785 0.0038 0.1177 78 F 0.9166 0.0035 0.0800 79 Q 0.9233 0.0033 0.0734 80 V 0.9122 0.0036 0.0842 81 A 0.8387 0.0044 0.1568 82 T 0.4269 0.0230 0.5501 83 D 0.0872 0.0594 0.8534 84 D 0.0783 0.0171 0.9046 85 Q 0.0055 0.9063 0.0882 86 A 0.0048 0.9527 0.0425 87 E 0.0047 0.9570 0.0382 88 T 0.0047 0.9588 0.0365 89 D 0.0047 0.9595 0.0358 90 R 0.0046 0.9564 0.0390 91 L 0.0047 0.9542 0.0411 92 W 0.0047 0.9592 0.0362 93 N 0.0047 0.9601 0.0352 94 A 0.0047 0.9577 0.0376 95 I 0.0048 0.9490 0.0462 96 V 0.0050 0.9177 0.0773 97 D 0.0070 0.8002 0.1928 98 N 0.0440 0.4482 0.5078 99 G 0.0507 0.0463 0.9030 100 G 0.0501 0.0482 0.9017 101 E 0.1152 0.1526 0.7321 102 E 0.1301 0.2522 0.6177 103 S 0.1669 0.2253 0.6078 104 A 0.3480 0.1323 0.5197 105 C 0.6264 0.0424 0.3311 106 G 0.7361 0.0193 0.2447 107 W 0.8567 0.0099 0.1334 108 C 0.8922 0.0073 0.1005 109 R 0.8630 0.0088 0.1282 110 D 0.4800 0.0173 0.5026 111 K 0.0553 0.0848 0.8599 112 W 0.0669 0.0391 0.8940 113 G 0.1515 0.0413 0.8073 114 I 0.5230 0.0164 0.4606 115 S 0.8192 0.0149 0.1659 116 W 0.8718 0.0137 0.1145 117 Q 0.8797 0.0115 0.1088 118 I 0.8353 0.0163 0.1483 119 T 0.5044 0.0217 0.4739 120 P 0.2494 0.1730 0.5776 121 R 0.1435 0.4224 0.4341 122 V 0.1049 0.5791 0.3159 123 L 0.0483 0.7172 0.2345 124 S 0.0273 0.7982 0.1745 125 E 0.0217 0.7979 0.1805 126 A 0.0315 0.7517 0.2168 127 I 0.0555 0.5471 0.3975 128 A 0.0473 0.3694 0.5833 129 S 0.0679 0.0660 0.8660 130 P 0.0226 0.3187 0.6588 131 D 0.0541 0.3375 0.6085 132 R 0.0049 0.9381 0.0571 133 A 0.0047 0.9583 0.0370 134 A 0.0047 0.9576 0.0377 135 A 0.0047 0.9565 0.0388 136 R 0.0047 0.9576 0.0377 137 R 0.0046 0.9548 0.0405 138 A 0.0047 0.9554 0.0399 139 F 0.0047 0.9592 0.0361 140 E 0.0047 0.9599 0.0354 141 A 0.0048 0.9539 0.0412 142 M 0.0049 0.9346 0.0604 143 M 0.0068 0.8637 0.1295 144 T 0.0100 0.6281 0.3618 145 M 0.0555 0.2917 0.6528 146 G 0.0333 0.1506 0.8160 147 R 0.1657 0.1679 0.6665 148 I 0.2434 0.0779 0.6787 149 D 0.2486 0.1025 0.6489 150 I 0.0084 0.9347 0.0569 151 A 0.0071 0.9535 0.0394 152 T 0.0059 0.9547 0.0394 153 I 0.0053 0.9531 0.0417 154 E 0.0048 0.9576 0.0376 155 K 0.0050 0.9518 0.0432 156 A 0.0068 0.9197 0.0735 157 F 0.0119 0.8089 0.1791 158 K 0.0286 0.3668 0.6047 159 G 0.0270 0.0809 0.8921