# This file is the result of combining several RDB files, specifically # T0369.t04.dssp-ebghstl.rdb (weight 1.53986) # T0369.t04.stride-ebghtl.rdb (weight 1.24869) # T0369.t04.str2.rdb (weight 1.54758) # T0369.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 T0369.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.stride-ebghtl.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.str2.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.alpha.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0516 0.0977 0.8508 2 T 0.0520 0.2538 0.6941 3 D 0.0454 0.6036 0.3510 4 W 0.0062 0.9159 0.0778 5 Q 0.0052 0.9492 0.0457 6 Q 0.0047 0.9549 0.0404 7 A 0.0048 0.9562 0.0391 8 L 0.0048 0.9537 0.0415 9 D 0.0050 0.9463 0.0486 10 R 0.0057 0.9284 0.0659 11 H 0.0075 0.8997 0.0928 12 V 0.0287 0.8403 0.1310 13 G 0.0181 0.7960 0.1859 14 V 0.0297 0.7969 0.1734 15 G 0.0309 0.7803 0.1888 16 V 0.0259 0.8786 0.0955 17 R 0.0247 0.8875 0.0878 18 T 0.0156 0.9046 0.0798 19 T 0.0098 0.9293 0.0609 20 R 0.0052 0.9554 0.0394 21 D 0.0054 0.9571 0.0375 22 L 0.0051 0.9526 0.0423 23 I 0.0052 0.9301 0.0647 24 R 0.0064 0.7946 0.1989 25 L 0.0163 0.3324 0.6513 26 I 0.0691 0.0272 0.9038 27 Q 0.0562 0.0097 0.9341 28 P 0.0064 0.8201 0.1735 29 E 0.0064 0.8429 0.1507 30 D 0.0086 0.8393 0.1521 31 W 0.0243 0.6803 0.2955 32 D 0.0279 0.4376 0.5345 33 K 0.0660 0.2251 0.7090 34 R 0.0909 0.0331 0.8760 35 P 0.1021 0.0431 0.8549 36 I 0.0870 0.0531 0.8598 37 S 0.0436 0.1208 0.8355 38 G 0.0312 0.0925 0.8763 39 K 0.0894 0.0909 0.8197 40 R 0.1321 0.0673 0.8006 41 S 0.1452 0.1771 0.6777 42 V 0.0048 0.9516 0.0436 43 Y 0.0047 0.9603 0.0350 44 E 0.0047 0.9602 0.0352 45 V 0.0047 0.9597 0.0356 46 A 0.0047 0.9589 0.0365 47 V 0.0046 0.9582 0.0371 48 H 0.0047 0.9567 0.0386 49 L 0.0047 0.9553 0.0400 50 A 0.0047 0.9540 0.0413 51 V 0.0050 0.9486 0.0464 52 L 0.0065 0.9308 0.0628 53 L 0.0091 0.9086 0.0823 54 E 0.0143 0.9001 0.0856 55 A 0.0223 0.8912 0.0865 56 D 0.0176 0.8989 0.0835 57 L 0.0234 0.8940 0.0826 58 R 0.0301 0.8702 0.0997 59 I 0.0330 0.8493 0.1177 60 A 0.0469 0.7575 0.1956 61 T 0.0541 0.4431 0.5028 62 G 0.0376 0.1119 0.8504 63 A 0.0711 0.0771 0.8518 64 T 0.0996 0.0868 0.8136 65 A 0.0448 0.4368 0.5184 66 D 0.0295 0.6147 0.3558 67 E 0.0303 0.7414 0.2283 68 M 0.0569 0.6608 0.2823 69 A 0.0695 0.6167 0.3138 70 Q 0.0824 0.5782 0.3394 71 F 0.0934 0.4279 0.4787 72 Y 0.0928 0.2862 0.6210 73 A 0.1049 0.1638 0.7313 74 V 0.1060 0.0582 0.8359 75 P 0.0996 0.0478 0.8526 76 V 0.1236 0.0479 0.8286 77 L 0.0775 0.0342 0.8883 78 P 0.0067 0.9108 0.0825 79 E 0.0048 0.9463 0.0488 80 Q 0.0050 0.9477 0.0473 81 L 0.0049 0.9496 0.0455 82 V 0.0048 0.9526 0.0426 83 D 0.0049 0.9487 0.0464 84 R 0.0050 0.9428 0.0522 85 L 0.0052 0.9386 0.0563 86 D 0.0052 0.9414 0.0534 87 Q 0.0051 0.9360 0.0589 88 S 0.0052 0.9346 0.0602 89 W 0.0049 0.9498 0.0453 90 Q 0.0048 0.9468 0.0484 91 Y 0.0049 0.9444 0.0508 92 Y 0.0050 0.9285 0.0665 93 Q 0.0060 0.9079 0.0862 94 D 0.0080 0.8559 0.1360 95 R 0.0132 0.7840 0.2028 96 L 0.0226 0.6732 0.3042 97 M 0.0123 0.7960 0.1916 98 A 0.0098 0.7962 0.1940 99 D 0.0161 0.7447 0.2393 100 F 0.0248 0.6956 0.2795 101 S 0.0319 0.5621 0.4060 102 T 0.0653 0.4186 0.5162 103 E 0.1521 0.2714 0.5766 104 T 0.2147 0.1745 0.6108 105 T 0.1897 0.1551 0.6553 106 Y 0.1705 0.1826 0.6468 107 W 0.1181 0.1221 0.7598 108 G 0.0680 0.0625 0.8694 109 V 0.0937 0.0399 0.8664 110 T 0.1235 0.0574 0.8191 111 D 0.1122 0.1040 0.7837 112 S 0.0812 0.2864 0.6324 113 T 0.0111 0.9060 0.0830 114 T 0.0053 0.9505 0.0442 115 G 0.0048 0.9571 0.0382 116 W 0.0049 0.9588 0.0363 117 L 0.0047 0.9596 0.0357 118 L 0.0047 0.9596 0.0357 119 E 0.0049 0.9567 0.0383 120 A 0.0053 0.9499 0.0448 121 A 0.0062 0.9341 0.0597 122 V 0.0082 0.8913 0.1005 123 H 0.0130 0.8317 0.1553 124 L 0.0138 0.8417 0.1445 125 Y 0.0250 0.8123 0.1627 126 H 0.0256 0.7900 0.1844 127 H 0.0257 0.8214 0.1529 128 R 0.0071 0.9174 0.0755 129 S 0.0068 0.9412 0.0520 130 Q 0.0053 0.9543 0.0404 131 L 0.0047 0.9601 0.0353 132 L 0.0046 0.9610 0.0343 133 D 0.0047 0.9610 0.0343 134 Y 0.0047 0.9605 0.0348 135 L 0.0048 0.9590 0.0362 136 N 0.0052 0.9489 0.0460 137 L 0.0077 0.9016 0.0907 138 L 0.0444 0.4328 0.5228 139 G 0.0360 0.0284 0.9356 140 Y 0.0726 0.0165 0.9109 141 D 0.1949 0.0169 0.7882 142 I 0.1630 0.0312 0.8058 143 K 0.1318 0.0437 0.8245 144 L 0.0776 0.4151 0.5073 145 D 0.0873 0.4189 0.4938 146 L 0.1089 0.3933 0.4978 147 F 0.1371 0.0931 0.7697 148 E 0.0546 0.0623 0.8831