# This file is the result of combining several RDB files, specifically # T0370.t06.dssp-ebghstl.rdb (weight 1.53986) # T0370.t06.stride-ebghtl.rdb (weight 1.24869) # T0370.t06.str2.rdb (weight 1.54758) # T0370.t06.alpha.rdb (weight 0.659012) # T0370.t04.dssp-ebghstl.rdb (weight 1.53986) # T0370.t04.stride-ebghtl.rdb (weight 1.24869) # T0370.t04.str2.rdb (weight 1.54758) # T0370.t04.alpha.rdb (weight 0.659012) # T0370.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0370.t2k.stride-ebghtl.rdb (weight 1.24869) # T0370.t2k.str2.rdb (weight 1.54758) # T0370.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 T0370.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0370 # 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 T0370.t06-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 692 # # ============================================ # Comments from T0370.t06.stride-ebghtl.rdb # ============================================ # TARGET T0370 # Using neural net t06-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 T0370.t06-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 692 # # ============================================ # Comments from T0370.t06.str2.rdb # ============================================ # TARGET T0370 # 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 T0370.t06-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 692 # # ============================================ # Comments from T0370.t06.alpha.rdb # ============================================ # TARGET T0370 # Using neural net t06-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 T0370.t06-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 692 # # ============================================ # Comments from T0370.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.stride-ebghtl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.str2.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.alpha.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 34 # # ============================================ # Comments from T0370.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 34 # # ============================================ # Comments from T0370.t2k.str2.rdb # ============================================ # TARGET T0370 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0370.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 34 # # ============================================ # Comments from T0370.t2k.alpha.rdb # ============================================ # TARGET T0370 # 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 T0370.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 34 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0636 0.0432 0.8931 2 T 0.1116 0.0800 0.8084 3 T 0.0958 0.1070 0.7971 4 P 0.0773 0.1689 0.7538 5 P 0.0776 0.2045 0.7178 6 A 0.0893 0.1865 0.7242 7 R 0.0813 0.2090 0.7097 8 T 0.0851 0.2924 0.6224 9 A 0.1067 0.3829 0.5104 10 K 0.1343 0.3557 0.5100 11 Q 0.1331 0.2810 0.5859 12 R 0.1043 0.1397 0.7561 13 I 0.0623 0.1111 0.8265 14 Q 0.0091 0.8687 0.1222 15 D 0.0068 0.8974 0.0958 16 T 0.0063 0.9191 0.0746 17 L 0.0066 0.9307 0.0628 18 N 0.0079 0.9242 0.0679 19 R 0.0083 0.9074 0.0843 20 L 0.0111 0.8832 0.1057 21 E 0.0168 0.8084 0.1748 22 L 0.0239 0.5578 0.4183 23 D 0.0512 0.2440 0.7048 24 V 0.1030 0.0801 0.8169 25 D 0.1337 0.0607 0.8056 26 A 0.6284 0.0252 0.3464 27 W 0.8744 0.0069 0.1186 28 V 0.9187 0.0038 0.0775 29 S 0.9155 0.0044 0.0801 30 T 0.8937 0.0064 0.1000 31 A 0.8465 0.0065 0.1470 32 G 0.7371 0.0067 0.2562 33 A 0.2317 0.0145 0.7538 34 D 0.0267 0.1000 0.8733 35 G 0.0485 0.0201 0.9315 36 G 0.0726 0.0265 0.9009 37 A 0.2044 0.0107 0.7849 38 P 0.5421 0.0105 0.4475 39 Y 0.6959 0.0142 0.2899 40 L 0.8239 0.0056 0.1705 41 V 0.8182 0.0062 0.1756 42 P 0.8463 0.0049 0.1488 43 L 0.8952 0.0049 0.1000 44 S 0.9137 0.0048 0.0815 45 Y 0.9122 0.0043 0.0836 46 L 0.9073 0.0046 0.0881 47 W 0.8392 0.0093 0.1515 48 D 0.4717 0.0221 0.5061 49 G 0.0567 0.0691 0.8742 50 E 0.1372 0.0765 0.7863 51 T 0.8119 0.0122 0.1759 52 F 0.9118 0.0040 0.0842 53 L 0.9224 0.0042 0.0734 54 V 0.9130 0.0055 0.0815 55 A 0.8165 0.0127 0.1708 56 T 0.3861 0.0143 0.5996 57 P 0.0990 0.0624 0.8386 58 A 0.0344 0.1579 0.8077 59 A 0.0379 0.2140 0.7481 60 S 0.0590 0.3075 0.6335 61 P 0.0710 0.5908 0.3382 62 T 0.0939 0.6589 0.2472 63 G 0.0860 0.7580 0.1560 64 R 0.0806 0.7776 0.1419 65 N 0.0794 0.7434 0.1772 66 L 0.0739 0.7158 0.2103 67 S 0.0786 0.5830 0.3384 68 E 0.0675 0.3737 0.5587 69 T 0.0829 0.0372 0.8799 70 G 0.0525 0.0887 0.8588 71 R 0.3461 0.0452 0.6087 72 V 0.8307 0.0069 0.1624 73 R 0.9051 0.0051 0.0898 74 L 0.9232 0.0036 0.0732 75 G 0.9038 0.0037 0.0926 76 I 0.8235 0.0085 0.1679 77 G 0.4898 0.0228 0.4875 78 P 0.1675 0.0600 0.7725 79 T 0.0854 0.0773 0.8373 80 R 0.1272 0.0417 0.8311 81 D 0.2105 0.0372 0.7523 82 L 0.7364 0.0074 0.2562 83 V 0.8941 0.0036 0.1023 84 L 0.9175 0.0038 0.0787 85 V 0.9072 0.0042 0.0886 86 E 0.8404 0.0215 0.1381 87 G 0.7926 0.0087 0.1987 88 T 0.8092 0.0105 0.1804 89 A 0.8428 0.0082 0.1490 90 L 0.8558 0.0069 0.1374 91 P 0.8065 0.0081 0.1854 92 L 0.4843 0.0188 0.4969 93 E 0.1911 0.0388 0.7701 94 P 0.0720 0.0515 0.8765 95 A 0.0380 0.1509 0.8111 96 G 0.0417 0.2340 0.7243 97 L 0.0461 0.3952 0.5587 98 P 0.0312 0.5740 0.3949 99 D 0.0249 0.7281 0.2469 100 G 0.0139 0.8589 0.1272 101 V 0.0091 0.9108 0.0801 102 G 0.0079 0.9230 0.0690 103 D 0.0070 0.9307 0.0623 104 T 0.0066 0.9333 0.0601 105 F 0.0065 0.9299 0.0636 106 A 0.0067 0.9090 0.0842 107 E 0.0088 0.8463 0.1449 108 K 0.0197 0.7125 0.2678 109 T 0.0571 0.3976 0.5453 110 G 0.0724 0.1380 0.7896 111 F 0.0885 0.0950 0.8166 112 D 0.0867 0.0951 0.8181 113 P 0.0933 0.1634 0.7433 114 R 0.0934 0.2005 0.7061 115 R 0.0946 0.1524 0.7530 116 L 0.0932 0.1166 0.7902 117 T 0.0851 0.0770 0.8379 118 T 0.0858 0.0697 0.8446 119 S 0.1785 0.0694 0.7521 120 Y 0.5570 0.0196 0.4234 121 L 0.8323 0.0075 0.1602 122 Y 0.9186 0.0032 0.0783 123 F 0.9169 0.0039 0.0792 124 R 0.9224 0.0034 0.0743 125 I 0.8753 0.0056 0.1190 126 S 0.6196 0.0083 0.3721 127 P 0.3341 0.1149 0.5510 128 R 0.3883 0.1377 0.4740 129 R 0.6868 0.0703 0.2428 130 V 0.6938 0.0810 0.2251 131 Q 0.6204 0.1335 0.2461 132 A 0.5446 0.1769 0.2785 133 W 0.3242 0.3366 0.3392 134 R 0.2482 0.3179 0.4338 135 E 0.1260 0.3823 0.4917 136 A 0.0843 0.3175 0.5983 137 N 0.0546 0.3684 0.5769 138 E 0.0261 0.6686 0.3053 139 L 0.0256 0.8087 0.1657 140 S 0.0156 0.8443 0.1401 141 G 0.0127 0.8563 0.1310 142 R 0.0170 0.8798 0.1032 143 E 0.0151 0.8900 0.0949 144 L 0.0163 0.8440 0.1397 145 M 0.0254 0.7687 0.2059 146 R 0.0310 0.6811 0.2880 147 D 0.0639 0.4468 0.4893 148 G 0.0615 0.2077 0.7308 149 E 0.1284 0.1883 0.6833 150 W 0.2215 0.1678 0.6107 151 L 0.1613 0.1530 0.6857 152 V 0.1114 0.1351 0.7535 153 T 0.0728 0.0893 0.8378 154 D 0.0407 0.0456 0.9137