# This file is the result of combining several RDB files, specifically # T0157.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0157.t2k.stride-ebghtl.rdb (weight 1.24869) # T0157.t2k.str.rdb (weight 1.53983) # T0157.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 T0157.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0157 # 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 T0157.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 56 # # ============================================ # Comments from T0157.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0157 # 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 T0157.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 56 # # ============================================ # Comments from T0157.t2k.str.rdb # ============================================ # TARGET T0157 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0157.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 56 # # ============================================ # Comments from T0157.t2k.alpha.rdb # ============================================ # TARGET T0157 # 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 T0157.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 56 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0652 0.0445 0.8903 2 S 0.1199 0.0409 0.8392 3 G 0.2855 0.0374 0.6771 4 T 0.6861 0.0122 0.3016 5 L 0.8737 0.0079 0.1184 6 L 0.8939 0.0077 0.0985 7 A 0.8961 0.0076 0.0963 8 F 0.8576 0.0085 0.1339 9 D 0.5911 0.0100 0.3989 10 F 0.1927 0.0585 0.7488 11 G 0.0901 0.0518 0.8581 12 T 0.1960 0.0437 0.7603 13 K 0.4695 0.0177 0.5128 14 S 0.7759 0.0130 0.2111 15 I 0.8379 0.0162 0.1460 16 G 0.8530 0.0191 0.1280 17 V 0.8951 0.0107 0.0941 18 A 0.8806 0.0110 0.1084 19 V 0.8128 0.0173 0.1699 20 G 0.5599 0.0288 0.4113 21 Q 0.1937 0.0444 0.7619 22 R 0.0628 0.2578 0.6794 23 I 0.0407 0.2892 0.6701 24 T 0.0637 0.2909 0.6454 25 G 0.1313 0.2425 0.6263 26 T 0.3089 0.1902 0.5009 27 A 0.4389 0.1344 0.4267 28 R 0.4351 0.0883 0.4766 29 P 0.3713 0.1267 0.5020 30 L 0.3532 0.2504 0.3965 31 P 0.4032 0.2445 0.3522 32 A 0.5380 0.2126 0.2494 33 I 0.6465 0.1179 0.2355 34 K 0.6087 0.1160 0.2753 35 A 0.3181 0.2040 0.4779 36 Q 0.1223 0.1972 0.6805 37 D 0.0653 0.1271 0.8076 38 G 0.0584 0.1216 0.8200 39 T 0.0922 0.2157 0.6921 40 P 0.0674 0.5292 0.4033 41 D 0.0617 0.6010 0.3373 42 W 0.0059 0.9315 0.0626 43 N 0.0049 0.9487 0.0465 44 I 0.0045 0.9524 0.0430 45 I 0.0044 0.9571 0.0385 46 E 0.0045 0.9571 0.0385 47 R 0.0045 0.9530 0.0425 48 L 0.0046 0.9485 0.0469 49 L 0.0051 0.9388 0.0561 50 K 0.0055 0.9170 0.0775 51 E 0.0108 0.7592 0.2300 52 W 0.0517 0.4536 0.4947 53 Q 0.1000 0.0428 0.8571 54 P 0.1344 0.0359 0.8297 55 D 0.3467 0.0606 0.5927 56 E 0.8940 0.0066 0.0994 57 I 0.9298 0.0036 0.0665 58 I 0.9194 0.0044 0.0762 59 V 0.8532 0.0192 0.1276 60 G 0.5952 0.0170 0.3878 61 L 0.3093 0.0132 0.6776 62 P 0.2988 0.0215 0.6797 63 L 0.4669 0.0490 0.4841 64 N 0.1551 0.0396 0.8053 65 M 0.0470 0.0880 0.8650 66 D 0.0421 0.0446 0.9133 67 G 0.0328 0.0412 0.9260 68 T 0.1051 0.0408 0.8541 69 E 0.2573 0.0970 0.6457 70 Q 0.0931 0.1777 0.7292 71 P 0.0621 0.5994 0.3384 72 L 0.0236 0.8438 0.1326 73 T 0.0098 0.9250 0.0652 74 A 0.0049 0.9547 0.0404 75 R 0.0049 0.9535 0.0416 76 A 0.0044 0.9584 0.0372 77 R 0.0044 0.9602 0.0355 78 K 0.0044 0.9597 0.0359 79 F 0.0044 0.9580 0.0376 80 A 0.0044 0.9584 0.0372 81 N 0.0044 0.9564 0.0392 82 R 0.0045 0.9497 0.0458 83 I 0.0047 0.9392 0.0561 84 H 0.0051 0.8968 0.0981 85 G 0.0068 0.7865 0.2067 86 R 0.0161 0.6360 0.3479 87 F 0.0863 0.2566 0.6571 88 G 0.0463 0.0321 0.9217 89 V 0.1059 0.0100 0.8841 90 E 0.4236 0.0065 0.5699 91 V 0.8620 0.0041 0.1339 92 K 0.9071 0.0059 0.0870 93 L 0.8834 0.0079 0.1087 94 H 0.7639 0.0294 0.2068 95 D 0.4541 0.0380 0.5079 96 E 0.1265 0.1219 0.7516 97 R 0.0857 0.1960 0.7184 98 L 0.0590 0.3308 0.6102 99 S 0.0500 0.4206 0.5294 100 T 0.0233 0.8046 0.1722 101 V 0.0066 0.9449 0.0485 102 E 0.0050 0.9570 0.0380 103 A 0.0044 0.9583 0.0373 104 R 0.0044 0.9581 0.0375 105 S 0.0047 0.9528 0.0425 106 G 0.0047 0.9480 0.0473 107 L 0.0054 0.9431 0.0516 108 F 0.0056 0.9317 0.0628 109 E 0.0062 0.8705 0.1233 110 Q 0.0434 0.3559 0.6007 111 G 0.0434 0.0283 0.9284 112 G 0.0747 0.0428 0.8825 113 Y 0.1089 0.1020 0.7891 114 R 0.0447 0.5742 0.3811 115 A 0.0349 0.6573 0.3078 116 L 0.0364 0.6531 0.3105 117 N 0.0467 0.5696 0.3837 118 K 0.0336 0.4979 0.4685 119 G 0.0284 0.4649 0.5067 120 K 0.0380 0.5725 0.3896 121 V 0.0328 0.7124 0.2548 122 D 0.0247 0.8162 0.1592 123 S 0.0060 0.9474 0.0466 124 A 0.0050 0.9574 0.0377 125 S 0.0044 0.9584 0.0372 126 A 0.0044 0.9590 0.0366 127 V 0.0043 0.9603 0.0354 128 I 0.0044 0.9598 0.0359 129 I 0.0044 0.9579 0.0377 130 L 0.0044 0.9523 0.0433 131 E 0.0045 0.9394 0.0561 132 S 0.0050 0.9185 0.0765 133 Y 0.0060 0.9040 0.0900 134 F 0.0088 0.8437 0.1475 135 E 0.0118 0.7032 0.2850 136 Q 0.0254 0.4004 0.5742 137 G 0.0421 0.1497 0.8083 138 Y 0.0437 0.0368 0.9194