# This file is the result of combining several RDB files, specifically # T0304.t04.dssp-ebghstl.rdb (weight 1.53986) # T0304.t04.stride-ebghtl.rdb (weight 1.24869) # T0304.t04.str2.rdb (weight 1.54758) # T0304.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 T0304.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t04.stride-ebghtl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t04.str2.rdb # ============================================ # TARGET T0304 # Using neural net t06-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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t04.alpha.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0908 0.0623 0.8469 2 S 0.1328 0.1269 0.7403 3 D 0.1485 0.1754 0.6760 4 T 0.1734 0.1323 0.6943 5 L 0.1533 0.0560 0.7907 6 P 0.0619 0.1013 0.8368 7 G 0.0705 0.0823 0.8471 8 T 0.2647 0.0549 0.6803 9 T 0.3690 0.0318 0.5993 10 L 0.2124 0.0205 0.7671 11 P 0.1179 0.0404 0.8417 12 D 0.0613 0.1490 0.7897 13 D 0.0570 0.1854 0.7576 14 N 0.0638 0.1841 0.7521 15 H 0.0957 0.1148 0.7895 16 D 0.1175 0.0846 0.7979 17 R 0.1298 0.0527 0.8175 18 P 0.1388 0.1480 0.7131 19 W 0.2435 0.2283 0.5281 20 W 0.2901 0.1603 0.5496 21 G 0.2234 0.0785 0.6981 22 L 0.2470 0.0274 0.7255 23 P 0.2535 0.0413 0.7052 24 C 0.2681 0.0796 0.6523 25 T 0.3043 0.0797 0.6161 26 V 0.4061 0.0524 0.5415 27 T 0.2961 0.0413 0.6626 28 P 0.1755 0.1883 0.6362 29 C 0.2101 0.2160 0.5740 30 F 0.2517 0.2754 0.4729 31 G 0.2708 0.2500 0.4792 32 A 0.3385 0.3283 0.3332 33 R 0.4363 0.3847 0.1790 34 L 0.5341 0.3539 0.1120 35 V 0.4974 0.3580 0.1446 36 Q 0.4216 0.3451 0.2333 37 E 0.1790 0.3089 0.5122 38 G 0.0549 0.1385 0.8066 39 N 0.0923 0.1454 0.7623 40 R 0.2751 0.3013 0.4236 41 L 0.4253 0.2988 0.2759 42 H 0.3903 0.3517 0.2580 43 Y 0.4430 0.3769 0.1801 44 L 0.3621 0.4190 0.2189 45 A 0.2461 0.4296 0.3243 46 D 0.2393 0.4095 0.3513 47 R 0.2304 0.3952 0.3744 48 A 0.3093 0.1727 0.5180 49 G 0.3895 0.0947 0.5158 50 I 0.6084 0.0562 0.3355 51 R 0.5810 0.0707 0.3483 52 G 0.6017 0.0325 0.3658 53 L 0.5945 0.0302 0.3753 54 F 0.4058 0.0281 0.5660 55 S 0.1728 0.0378 0.7893 56 D 0.0369 0.5455 0.4176 57 A 0.0178 0.7323 0.2499 58 D 0.0264 0.7454 0.2283 59 A 0.0531 0.7605 0.1864 60 Y 0.0548 0.7404 0.2048 61 H 0.0532 0.7350 0.2118 62 L 0.0188 0.8386 0.1426 63 D 0.0105 0.8784 0.1111 64 Q 0.0061 0.9007 0.0932 65 A 0.0059 0.8920 0.1021 66 F 0.0049 0.9052 0.0899 67 P 0.0047 0.9531 0.0422 68 L 0.0047 0.9579 0.0374 69 L 0.0047 0.9593 0.0360 70 M 0.0047 0.9603 0.0351 71 K 0.0047 0.9593 0.0360 72 Q 0.0047 0.9555 0.0399 73 L 0.0047 0.9517 0.0436 74 E 0.0051 0.9450 0.0500 75 L 0.0058 0.9312 0.0630 76 M 0.0079 0.8989 0.0933 77 L 0.0299 0.7686 0.2015 78 T 0.0481 0.5559 0.3959 79 S 0.0654 0.3203 0.6143 80 G 0.0655 0.1511 0.7834 81 E 0.1892 0.1091 0.7017 82 L 0.3227 0.0448 0.6325 83 N 0.1466 0.0147 0.8387 84 P 0.0251 0.3159 0.6590 85 R 0.0319 0.3244 0.6437 86 H 0.1130 0.2576 0.6294 87 Q 0.2355 0.0872 0.6773 88 H 0.4388 0.0449 0.5164 89 T 0.7923 0.0152 0.1925 90 V 0.8794 0.0087 0.1119 91 T 0.8819 0.0117 0.1065 92 L 0.8348 0.0198 0.1454 93 Y 0.7090 0.0281 0.2629 94 A 0.4460 0.0685 0.4855 95 K 0.1077 0.0851 0.8072 96 G 0.1393 0.0488 0.8119 97 L 0.4216 0.0254 0.5530 98 T 0.6518 0.0258 0.3223 99 C 0.6254 0.0608 0.3138 100 K 0.5304 0.0980 0.3716 101 A 0.4316 0.1164 0.4521 102 D 0.4138 0.1096 0.4767 103 T 0.4225 0.1179 0.4596 104 L 0.2979 0.1333 0.5688 105 S 0.1865 0.1213 0.6921 106 S 0.1888 0.1126 0.6986 107 C 0.1635 0.1048 0.7317 108 D 0.2537 0.0573 0.6890 109 Y 0.7364 0.0113 0.2523 110 V 0.9148 0.0039 0.0813 111 Y 0.9274 0.0047 0.0679 112 L 0.9267 0.0054 0.0679 113 A 0.9212 0.0045 0.0743 114 V 0.8899 0.0073 0.1029 115 Y 0.7394 0.0067 0.2538 116 P 0.3893 0.0184 0.5922 117 T 0.1374 0.0336 0.8290 118 P 0.0391 0.2875 0.6734 119 E 0.0483 0.3133 0.6384 120 M 0.0912 0.2115 0.6973 121 K 0.0744 0.1031 0.8225 122 N 0.0495 0.0421 0.9084