# This file is the result of combining several RDB files, specifically # T0602.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0602.t2k.stride-ebghtl.rdb (weight 1.24869) # T0602.t2k.str2.rdb (weight 1.54758) # T0602.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 T0602.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0602 # 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 T0602.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 75 # # ============================================ # Comments from T0602.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0602 # 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 T0602.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 75 # # ============================================ # Comments from T0602.t2k.str2.rdb # ============================================ # TARGET T0602 # 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 T0602.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 75 # # ============================================ # Comments from T0602.t2k.alpha.rdb # ============================================ # TARGET T0602 # 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 T0602.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 75 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0607 0.1598 0.7795 2 N 0.0728 0.2540 0.6732 3 A 0.0535 0.2759 0.6705 4 M 0.0514 0.2603 0.6882 5 E 0.0322 0.2703 0.6975 6 R 0.0520 0.2178 0.7303 7 H 0.0207 0.6135 0.3659 8 Q 0.0106 0.8492 0.1402 9 H 0.0069 0.8975 0.0956 10 L 0.0052 0.9299 0.0650 11 L 0.0048 0.9464 0.0488 12 S 0.0048 0.9468 0.0484 13 E 0.0048 0.9522 0.0430 14 Y 0.0047 0.9568 0.0385 15 Q 0.0047 0.9561 0.0392 16 Q 0.0048 0.9492 0.0460 17 I 0.0049 0.9462 0.0489 18 L 0.0049 0.9415 0.0536 19 T 0.0052 0.9018 0.0930 20 L 0.0074 0.8643 0.1283 21 S 0.0134 0.8670 0.1195 22 E 0.0048 0.9517 0.0435 23 Q 0.0047 0.9567 0.0387 24 M 0.0047 0.9586 0.0367 25 L 0.0047 0.9586 0.0367 26 V 0.0047 0.9569 0.0384 27 L 0.0047 0.9501 0.0452 28 A 0.0049 0.9183 0.0768 29 T 0.0056 0.8192 0.1752 30 E 0.0448 0.4802 0.4750 31 G 0.0405 0.2468 0.7127 32 N 0.0617 0.2700 0.6682 33 W 0.0097 0.8388 0.1514 34 D 0.0052 0.9395 0.0553 35 A 0.0048 0.9516 0.0436 36 L 0.0047 0.9573 0.0379 37 V 0.0048 0.9569 0.0382 38 D 0.0048 0.9521 0.0430 39 L 0.0048 0.9477 0.0474 40 E 0.0049 0.9535 0.0416 41 M 0.0049 0.9568 0.0383 42 T 0.0048 0.9551 0.0401 43 Y 0.0047 0.9559 0.0393 44 L 0.0047 0.9586 0.0367 45 K 0.0047 0.9587 0.0366 46 A 0.0047 0.9565 0.0387 47 V 0.0047 0.9560 0.0392 48 E 0.0048 0.9530 0.0422 49 S 0.0051 0.9389 0.0561 50 T 0.0062 0.9168 0.0770 51 A 0.0098 0.8584 0.1318 52 N 0.0142 0.6720 0.3138 53 I 0.0524 0.3577 0.5899 54 T 0.0595 0.1772 0.7633 55 I 0.0627 0.1536 0.7837 56 S 0.0614 0.1337 0.8049 57 S 0.0572 0.1495 0.7933 58 C 0.0622 0.0980 0.8397 59 S 0.0628 0.0942 0.8429 60 S 0.0503 0.1272 0.8224 61 L 0.0077 0.8863 0.1060 62 M 0.0058 0.9258 0.0684 63 L 0.0055 0.9336 0.0609 64 Q 0.0051 0.9449 0.0501 65 D 0.0056 0.9399 0.0546 66 L 0.0062 0.9330 0.0609 67 L 0.0054 0.9357 0.0589 68 R 0.0057 0.9471 0.0472 69 E 0.0049 0.9477 0.0474 70 K 0.0048 0.9516 0.0437 71 L 0.0047 0.9550 0.0402 72 R 0.0047 0.9567 0.0385 73 A 0.0048 0.9512 0.0440 74 I 0.0048 0.9434 0.0518 75 L 0.0057 0.9241 0.0701 76 D 0.0084 0.8364 0.1552 77 N 0.0255 0.6257 0.3488 78 E 0.0065 0.9118 0.0817 79 I 0.0056 0.9458 0.0486 80 E 0.0049 0.9514 0.0437 81 I 0.0048 0.9530 0.0422 82 K 0.0048 0.9492 0.0460 83 R 0.0051 0.9373 0.0576 84 L 0.0054 0.9156 0.0789 85 L 0.0066 0.9039 0.0895 86 Q 0.0071 0.9224 0.0705 87 L 0.0066 0.9222 0.0712 88 R 0.0080 0.9190 0.0729 89 L 0.0055 0.9455 0.0490 90 D 0.0054 0.9471 0.0476 91 R 0.0052 0.9438 0.0510 92 L 0.0048 0.9479 0.0473 93 S 0.0049 0.9487 0.0464 94 D 0.0050 0.9302 0.0649 95 L 0.0061 0.8982 0.0957 96 V 0.0142 0.8162 0.1696 97 G 0.0137 0.5598 0.4266 98 Q 0.0171 0.5528 0.4301 99 S 0.0383 0.5702 0.3915 100 T 0.0248 0.6903 0.2849 101 K 0.0229 0.8051 0.1720 102 Q 0.0294 0.8702 0.1005 103 Q 0.0247 0.8966 0.0787 104 A 0.0301 0.8965 0.0735 105 V 0.0305 0.8897 0.0798 106 N 0.0414 0.8460 0.1126 107 N 0.0389 0.8129 0.1482 108 T 0.0448 0.7136 0.2416 109 Y 0.0573 0.5362 0.4065 110 G 0.0585 0.3467 0.5948 111 Q 0.1056 0.2740 0.6204 112 F 0.1368 0.1297 0.7335 113 P 0.0521 0.1040 0.8438 114 D 0.0506 0.0824 0.8670 115 H 0.2659 0.0880 0.6461 116 A 0.5409 0.0546 0.4045 117 L 0.5028 0.0522 0.4450 118 L 0.2923 0.0240 0.6838 119 L 0.1228 0.1081 0.7690 120 G 0.0668 0.0845 0.8487 121 E 0.0927 0.0628 0.8446 122 T 0.0914 0.0494 0.8592 123 Q 0.0502 0.0441 0.9057