# This file is the result of combining several RDB files, specifically # T0155.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0155.t2k.stride-ebghtl.rdb (weight 1.24869) # T0155.t2k.str.rdb (weight 1.53983) # T0155.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 T0155.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0155 # 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 T0155.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 49 # # ============================================ # Comments from T0155.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0155 # 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 T0155.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 49 # # ============================================ # Comments from T0155.t2k.str.rdb # ============================================ # TARGET T0155 # 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 T0155.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 49 # # ============================================ # Comments from T0155.t2k.alpha.rdb # ============================================ # TARGET T0155 # 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 T0155.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 49 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0680 0.0512 0.8808 2 A 0.1884 0.0623 0.7493 3 D 0.2679 0.0729 0.6592 4 R 0.7101 0.0314 0.2586 5 I 0.8733 0.0081 0.1186 6 E 0.8995 0.0068 0.0937 7 L 0.8729 0.0088 0.1183 8 R 0.6236 0.0443 0.3321 9 G 0.4740 0.0244 0.5016 10 L 0.7936 0.0052 0.2012 11 T 0.8980 0.0049 0.0971 12 V 0.9176 0.0040 0.0784 13 H 0.8856 0.0137 0.1007 14 G 0.8776 0.0075 0.1149 15 R 0.8493 0.0172 0.1335 16 H 0.6790 0.0347 0.2863 17 G 0.4102 0.0400 0.5498 18 V 0.2554 0.0545 0.6902 19 Y 0.1560 0.0885 0.7555 20 D 0.0360 0.6484 0.3156 21 H 0.0154 0.7892 0.1954 22 E 0.0168 0.8362 0.1469 23 R 0.0228 0.7631 0.2142 24 V 0.0304 0.6331 0.3365 25 A 0.0550 0.2505 0.6945 26 G 0.0450 0.0310 0.9241 27 Q 0.1113 0.0113 0.8774 28 R 0.4204 0.0075 0.5720 29 F 0.7856 0.0048 0.2097 30 V 0.9019 0.0036 0.0945 31 I 0.9137 0.0039 0.0825 32 D 0.9115 0.0043 0.0842 33 V 0.9058 0.0042 0.0900 34 T 0.8959 0.0074 0.0967 35 V 0.8710 0.0103 0.1187 36 W 0.8051 0.0114 0.1835 37 I 0.6729 0.0213 0.3058 38 D 0.3741 0.0201 0.6058 39 L 0.0393 0.4833 0.4773 40 A 0.0146 0.6083 0.3771 41 E 0.0153 0.6701 0.3146 42 A 0.0322 0.5625 0.4053 43 A 0.0468 0.4216 0.5316 44 N 0.0665 0.3381 0.5954 45 S 0.0727 0.2676 0.6597 46 D 0.0460 0.2756 0.6784 47 D 0.0635 0.2647 0.6718 48 L 0.0423 0.6118 0.3459 49 A 0.0265 0.6747 0.2988 50 D 0.0290 0.6477 0.3234 51 T 0.0915 0.4938 0.4147 52 Y 0.2023 0.3072 0.4905 53 D 0.1344 0.2659 0.5997 54 Y 0.0053 0.9323 0.0624 55 V 0.0045 0.9538 0.0417 56 R 0.0045 0.9573 0.0383 57 L 0.0044 0.9577 0.0378 58 A 0.0044 0.9590 0.0366 59 S 0.0044 0.9579 0.0377 60 R 0.0044 0.9558 0.0398 61 A 0.0047 0.9555 0.0398 62 A 0.0047 0.9570 0.0383 63 E 0.0046 0.9512 0.0443 64 I 0.0055 0.9331 0.0614 65 V 0.0078 0.8922 0.0999 66 A 0.0189 0.6864 0.2947 67 G 0.0325 0.2798 0.6877 68 P 0.0496 0.1073 0.8430 69 P 0.0429 0.3354 0.6218 70 R 0.0273 0.7249 0.2478 71 K 0.0259 0.7768 0.1973 72 L 0.0235 0.8337 0.1428 73 I 0.0065 0.9437 0.0498 74 E 0.0054 0.9500 0.0446 75 T 0.0050 0.9517 0.0433 76 V 0.0047 0.9527 0.0426 77 G 0.0047 0.9529 0.0424 78 A 0.0048 0.9496 0.0456 79 E 0.0049 0.9487 0.0464 80 I 0.0046 0.9494 0.0460 81 A 0.0046 0.9407 0.0546 82 D 0.0048 0.9319 0.0633 83 H 0.0058 0.8997 0.0945 84 V 0.0113 0.8411 0.1476 85 M 0.0166 0.6100 0.3734 86 D 0.0282 0.3540 0.6178 87 D 0.0626 0.1165 0.8210 88 Q 0.0392 0.1198 0.8409 89 R 0.0980 0.0955 0.8065 90 V 0.3655 0.0215 0.6130 91 H 0.5870 0.0200 0.3930 92 A 0.8739 0.0042 0.1218 93 V 0.9055 0.0039 0.0906 94 E 0.9221 0.0036 0.0743 95 V 0.9145 0.0037 0.0818 96 A 0.9050 0.0041 0.0909 97 V 0.8398 0.0057 0.1545 98 H 0.5658 0.0135 0.4207 99 K 0.3000 0.0171 0.6830 100 P 0.1053 0.0646 0.8301 101 Q 0.0883 0.0490 0.8626 102 A 0.0969 0.0465 0.8566 103 P 0.1048 0.0646 0.8306 104 I 0.1452 0.0913 0.7635 105 P 0.1167 0.1705 0.7128 106 Q 0.0984 0.2388 0.6628 107 T 0.1279 0.2482 0.6239 108 F 0.2008 0.2218 0.5774 109 D 0.1742 0.1807 0.6451 110 D 0.2692 0.0757 0.6551 111 V 0.5324 0.0092 0.4584 112 A 0.7545 0.0052 0.2403 113 V 0.9101 0.0038 0.0862 114 V 0.9249 0.0036 0.0716 115 I 0.9183 0.0034 0.0783 116 R 0.8806 0.0042 0.1152 117 R 0.7753 0.0062 0.2186 118 S 0.5200 0.0181 0.4619 119 R 0.2308 0.0376 0.7316 120 R 0.0978 0.0641 0.8381 121 G 0.1084 0.0458 0.8458 122 G 0.1622 0.0390 0.7988 123 R 0.2831 0.0346 0.6824 124 G 0.4894 0.0300 0.4806 125 W 0.6798 0.0246 0.2956 126 V 0.7386 0.0214 0.2400 127 V 0.6163 0.0245 0.3591 128 P 0.3610 0.0392 0.5998 129 A 0.1327 0.0968 0.7705 130 G 0.0803 0.0891 0.8307 131 G 0.0877 0.0936 0.8186 132 A 0.1269 0.0874 0.7857 133 V 0.0598 0.0387 0.9015