# This file is the result of combining several RDB files, specifically # T0350.t04.dssp-ebghstl.rdb (weight 1.53986) # T0350.t04.stride-ebghtl.rdb (weight 1.24869) # T0350.t04.str2.rdb (weight 1.54758) # T0350.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 T0350.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.stride-ebghtl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.str2.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.alpha.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1033 0.0133 0.8834 2 N 0.1298 0.0144 0.8559 3 I 0.1006 0.3313 0.5680 4 E 0.1311 0.3260 0.5428 5 R 0.1889 0.3671 0.4439 6 L 0.2188 0.2086 0.5726 7 T 0.2112 0.1920 0.5968 8 T 0.1959 0.1993 0.6048 9 L 0.1730 0.1762 0.6508 10 Q 0.1220 0.1263 0.7517 11 P 0.1140 0.1805 0.7055 12 V 0.1185 0.2606 0.6208 13 W 0.1210 0.2183 0.6607 14 D 0.0861 0.2279 0.6859 15 R 0.0541 0.4787 0.4672 16 Y 0.0669 0.4254 0.5076 17 D 0.0643 0.4231 0.5126 18 T 0.0703 0.5437 0.3860 19 Q 0.1077 0.5192 0.3731 20 I 0.1262 0.4936 0.3802 21 H 0.1469 0.4002 0.4530 22 N 0.1396 0.3234 0.5369 23 Q 0.1001 0.3166 0.5832 24 K 0.0868 0.3246 0.5886 25 D 0.0825 0.3036 0.6139 26 N 0.0705 0.2894 0.6401 27 D 0.0706 0.2614 0.6680 28 N 0.0933 0.1611 0.7456 29 E 0.1087 0.0981 0.7932 30 V 0.1124 0.0314 0.8563 31 P 0.1052 0.0413 0.8535 32 V 0.1063 0.1603 0.7334 33 H 0.1356 0.1539 0.7106 34 Q 0.1703 0.1167 0.7130 35 V 0.1736 0.0348 0.7916 36 S 0.0842 0.0224 0.8934 37 Y 0.0054 0.9266 0.0680 38 T 0.0051 0.9442 0.0507 39 N 0.0051 0.9470 0.0479 40 L 0.0047 0.9589 0.0364 41 A 0.0047 0.9610 0.0343 42 E 0.0047 0.9596 0.0358 43 M 0.0047 0.9582 0.0371 44 V 0.0047 0.9599 0.0355 45 G 0.0047 0.9572 0.0382 46 E 0.0047 0.9490 0.0462 47 M 0.0048 0.9393 0.0559 48 N 0.0057 0.9123 0.0820 49 K 0.0080 0.8393 0.1527 50 L 0.0177 0.7338 0.2485 51 L 0.0913 0.3278 0.5808 52 E 0.0974 0.0982 0.8044 53 P 0.0766 0.2229 0.7006 54 S 0.1126 0.1771 0.7102 55 Q 0.2564 0.0970 0.6466 56 V 0.6304 0.0222 0.3474 57 H 0.8087 0.0072 0.1842 58 L 0.8771 0.0038 0.1191 59 K 0.9127 0.0038 0.0835 60 F 0.9165 0.0039 0.0796 61 E 0.9070 0.0046 0.0884 62 L 0.8815 0.0074 0.1112 63 H 0.6394 0.0103 0.3503 64 D 0.0700 0.2388 0.6912 65 K 0.0644 0.2636 0.6720 66 L 0.0834 0.1747 0.7419 67 N 0.1049 0.0412 0.8539 68 E 0.4360 0.0140 0.5500 69 Y 0.8392 0.0038 0.1570 70 Y 0.9091 0.0036 0.0873 71 V 0.9226 0.0037 0.0737 72 K 0.9289 0.0035 0.0676 73 V 0.9239 0.0033 0.0729 74 I 0.8893 0.0050 0.1057 75 E 0.6827 0.0079 0.3095 76 D 0.0641 0.1069 0.8290 77 S 0.0278 0.1284 0.8437 78 T 0.0797 0.0912 0.8291 79 N 0.0850 0.0836 0.8313 80 E 0.4929 0.0975 0.4096 81 V 0.7791 0.0828 0.1381 82 I 0.7868 0.0761 0.1370 83 R 0.7930 0.0537 0.1533 84 E 0.6932 0.0431 0.2637 85 I 0.2476 0.0193 0.7332 86 P 0.0761 0.0109 0.9130 87 P 0.0108 0.8884 0.1008 88 K 0.0048 0.9512 0.0440 89 R 0.0048 0.9556 0.0397 90 W 0.0049 0.9562 0.0389 91 L 0.0047 0.9606 0.0348 92 D 0.0046 0.9606 0.0348 93 F 0.0047 0.9587 0.0366 94 Y 0.0047 0.9572 0.0380 95 A 0.0048 0.9496 0.0456 96 A 0.0054 0.9230 0.0716 97 M 0.0056 0.9176 0.0767 98 T 0.0065 0.9051 0.0884 99 E 0.0066 0.8915 0.1019 100 F 0.0141 0.8533 0.1326 101 L 0.0200 0.8115 0.1685 102 G 0.0239 0.7261 0.2499 103 L 0.0506 0.7429 0.2065 104 F 0.0970 0.6992 0.2038 105 V 0.1243 0.6155 0.2602 106 D 0.1410 0.5189 0.3401 107 E 0.0296 0.7841 0.1863 108 K 0.0347 0.7471 0.2181 109 K 0.0503 0.6772 0.2725 110 L 0.0643 0.5092 0.4265 111 E 0.0621 0.3818 0.5561 112 H 0.0338 0.5228 0.4434 113 H 0.0347 0.3919 0.5734 114 H 0.0557 0.2674 0.6769 115 H 0.0764 0.1326 0.7910 116 H 0.0678 0.0737 0.8585 117 H 0.0413 0.0668 0.8919