# This file is the result of combining several RDB files, specifically # T0404.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0404.t2k.stride-ebghtl.rdb (weight 1.24869) # T0404.t2k.str2.rdb (weight 1.54758) # T0404.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 T0404.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0404 # 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 T0404.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 T0404.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0404 # 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 T0404.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 T0404.t2k.str2.rdb # ============================================ # TARGET T0404 # 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 T0404.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 T0404.t2k.alpha.rdb # ============================================ # TARGET T0404 # 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 T0404.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 0.0737 0.0292 0.8972 2 S 0.1789 0.0424 0.7786 3 K 0.2477 0.0471 0.7052 4 R 0.3260 0.0796 0.5944 5 A 0.3694 0.1110 0.5196 6 N 0.5522 0.1195 0.3283 7 K 0.7460 0.0911 0.1629 8 L 0.8158 0.0720 0.1122 9 V 0.8518 0.0608 0.0874 10 I 0.8655 0.0539 0.0807 11 V 0.8159 0.0743 0.1098 12 T 0.5290 0.1223 0.3488 13 E 0.1523 0.2334 0.6144 14 K 0.0473 0.6052 0.3475 15 V 0.0212 0.7327 0.2461 16 L 0.0192 0.7390 0.2418 17 L 0.0140 0.8465 0.1395 18 K 0.0150 0.8549 0.1301 19 K 0.0076 0.9189 0.0734 20 V 0.0053 0.9494 0.0453 21 A 0.0049 0.9579 0.0372 22 K 0.0047 0.9584 0.0369 23 I 0.0047 0.9581 0.0371 24 I 0.0048 0.9569 0.0383 25 E 0.0050 0.9482 0.0468 26 E 0.0055 0.9179 0.0766 27 A 0.0419 0.4266 0.5314 28 G 0.0497 0.0230 0.9274 29 A 0.0946 0.0108 0.8947 30 T 0.1496 0.0443 0.8061 31 G 0.5484 0.0414 0.4102 32 Y 0.8209 0.0097 0.1694 33 T 0.8853 0.0054 0.1093 34 V 0.8629 0.0080 0.1291 35 V 0.6954 0.0152 0.2894 36 D 0.4380 0.0277 0.5343 37 T 0.2987 0.0563 0.6451 38 G 0.1737 0.0409 0.7854 39 G 0.1677 0.0368 0.7955 40 K 0.2531 0.0478 0.6990 41 G 0.2038 0.0575 0.7387 42 S 0.1718 0.0814 0.7469 43 R 0.1394 0.0827 0.7779 44 N 0.1661 0.0740 0.7599 45 V 0.3725 0.0667 0.5607 46 R 0.4520 0.0689 0.4791 47 S 0.2720 0.1134 0.6146 48 T 0.1188 0.1345 0.7466 49 G 0.1120 0.1240 0.7639 50 K 0.2041 0.1256 0.6704 51 P 0.2235 0.1622 0.6142 52 N 0.2429 0.1670 0.5901 53 T 0.2305 0.1664 0.6031 54 S 0.2637 0.1764 0.5599 55 D 0.3259 0.1821 0.4920 56 T 0.3489 0.1781 0.4730 57 D 0.3043 0.2757 0.4200 58 S 0.2642 0.2863 0.4495 59 N 0.3396 0.1704 0.4900 60 V 0.4334 0.0910 0.4755 61 K 0.6669 0.0307 0.3025 62 F 0.8281 0.0132 0.1587 63 E 0.8915 0.0066 0.1019 64 V 0.9183 0.0046 0.0771 65 L 0.9025 0.0059 0.0917 66 T 0.8496 0.0052 0.1452 67 E 0.6228 0.0113 0.3659 68 N 0.1807 0.0101 0.8092 69 R 0.0212 0.6112 0.3677 70 E 0.0062 0.8574 0.1365 71 M 0.0058 0.8932 0.1010 72 A 0.0056 0.9020 0.0924 73 E 0.0062 0.9176 0.0762 74 K 0.0072 0.9141 0.0787 75 I 0.0060 0.9242 0.0698 76 A 0.0068 0.9265 0.0667 77 D 0.0054 0.9229 0.0717 78 Q 0.0062 0.8993 0.0945 79 V 0.0072 0.8556 0.1372 80 A 0.0086 0.8147 0.1768 81 I 0.0142 0.7472 0.2387 82 K 0.0134 0.7441 0.2424 83 F 0.0239 0.6702 0.3058 84 F 0.0558 0.4981 0.4461 85 T 0.0228 0.4367 0.5404 86 D 0.0231 0.2090 0.7679 87 Y 0.1828 0.0688 0.7483 88 A 0.4754 0.0265 0.4982 89 G 0.8542 0.0080 0.1378 90 I 0.9238 0.0040 0.0722 91 I 0.9227 0.0045 0.0728 92 Y 0.9179 0.0041 0.0780 93 I 0.8190 0.0112 0.1698 94 C 0.5929 0.0197 0.3874 95 E 0.4357 0.0305 0.5338 96 A 0.5739 0.0366 0.3895 97 E 0.7374 0.0324 0.2301 98 V 0.8001 0.0248 0.1751 99 L 0.6789 0.0319 0.2892 100 Y 0.4317 0.0217 0.5467 101 G 0.1434 0.2724 0.5843 102 R 0.1519 0.2708 0.5773 103 T 0.2837 0.2696 0.4466 104 F 0.3827 0.0665 0.5508 105 C 0.2746 0.0519 0.6735 106 G 0.1065 0.0523 0.8411 107 P 0.0487 0.1136 0.8377 108 D 0.0518 0.0825 0.8657 109 G 0.0534 0.0711 0.8755 110 C 0.0526 0.0425 0.9049