# This file is the result of combining several RDB files, specifically # T0269.t04.dssp-ebghstl.rdb (weight 1.53986) # T0269.t04.stride-ebghtl.rdb (weight 1.24869) # T0269.t04.str2.rdb (weight 1.54758) # T0269.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 T0269.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0269 # 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 T0269.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 2 # # ============================================ # Comments from T0269.t04.stride-ebghtl.rdb # ============================================ # TARGET T0269 # 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 T0269.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 2 # # ============================================ # Comments from T0269.t04.str2.rdb # ============================================ # TARGET T0269 # 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 T0269.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 2 # # ============================================ # Comments from T0269.t04.alpha.rdb # ============================================ # TARGET T0269 # 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 T0269.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0753 0.1172 0.8075 2 S 0.0815 0.2276 0.6909 3 L 0.1203 0.2618 0.6179 4 K 0.1457 0.2693 0.5849 5 R 0.3017 0.1481 0.5502 6 A 0.4157 0.0664 0.5179 7 V 0.3126 0.0320 0.6553 8 P 0.2007 0.0404 0.7589 9 A 0.1483 0.0970 0.7547 10 D 0.1318 0.0796 0.7886 11 W 0.0725 0.0720 0.8556 12 P 0.0512 0.1394 0.8094 13 N 0.0512 0.1327 0.8162 14 N 0.1024 0.1271 0.7705 15 E 0.3307 0.1354 0.5339 16 I 0.6859 0.0840 0.2301 17 I 0.6207 0.0779 0.3014 18 G 0.4110 0.0629 0.5261 19 E 0.3410 0.0785 0.5805 20 G 0.5929 0.0390 0.3681 21 L 0.7914 0.0134 0.1952 22 I 0.8433 0.0074 0.1493 23 V 0.6138 0.0084 0.3778 24 P 0.2110 0.0095 0.7795 25 P 0.0736 0.0184 0.9081 26 P 0.0673 0.0316 0.9012 27 T 0.0824 0.0330 0.8847 28 T 0.0620 0.0641 0.8739 29 E 0.0049 0.9050 0.0901 30 D 0.0047 0.9448 0.0505 31 Q 0.0048 0.9475 0.0477 32 A 0.0059 0.9446 0.0495 33 R 0.0060 0.9398 0.0542 34 A 0.0080 0.9091 0.0830 35 R 0.0121 0.8536 0.1343 36 M 0.0303 0.7470 0.2228 37 E 0.0368 0.6245 0.3387 38 S 0.0432 0.3222 0.6345 39 G 0.0353 0.0808 0.8839 40 Q 0.1432 0.0740 0.7828 41 Y 0.3885 0.0465 0.5650 42 R 0.4795 0.0604 0.4601 43 C 0.5397 0.0790 0.3814 44 L 0.5408 0.0792 0.3800 45 D 0.5611 0.0698 0.3690 46 W 0.6453 0.0980 0.2567 47 W 0.7505 0.0866 0.1630 48 F 0.7947 0.0695 0.1358 49 C 0.6963 0.0657 0.2380 50 W 0.3858 0.0678 0.5464 51 D 0.1580 0.0690 0.7730 52 T 0.1266 0.0323 0.8410 53 P 0.0982 0.0912 0.8106 54 A 0.1087 0.1030 0.7884 55 S 0.0866 0.1065 0.8070 56 R 0.0276 0.4716 0.5008 57 D 0.0279 0.4369 0.5352 58 D 0.0344 0.5323 0.4333 59 V 0.0059 0.9284 0.0656 60 E 0.0047 0.9547 0.0406 61 E 0.0047 0.9558 0.0396 62 A 0.0049 0.9522 0.0429 63 R 0.0047 0.9547 0.0406 64 R 0.0047 0.9524 0.0429 65 Y 0.0048 0.9493 0.0459 66 L 0.0055 0.9414 0.0532 67 R 0.0050 0.9400 0.0550 68 R 0.0065 0.9224 0.0711 69 A 0.0091 0.8685 0.1224 70 A 0.0156 0.7569 0.2275 71 E 0.0237 0.6483 0.3280 72 K 0.0472 0.3197 0.6331 73 P 0.0357 0.4522 0.5121 74 A 0.0375 0.6755 0.2869 75 K 0.0651 0.7471 0.1878 76 L 0.0857 0.7770 0.1373 77 L 0.0811 0.7768 0.1421 78 Y 0.0659 0.8073 0.1267 79 E 0.0401 0.8630 0.0969 80 E 0.0351 0.8494 0.1156 81 A 0.0350 0.8197 0.1453 82 R 0.0455 0.7442 0.2102 83 T 0.0615 0.6295 0.3090 84 H 0.0677 0.4577 0.4746 85 L 0.0818 0.2535 0.6647 86 H 0.0584 0.0761 0.8655