# This file is the result of combining several RDB files, specifically # T0156.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0156.t2k.stride-ebghtl.rdb (weight 1.24869) # T0156.t2k.str.rdb (weight 1.53983) # T0156.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 T0156.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0156 # 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 T0156.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 47 # # ============================================ # Comments from T0156.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0156 # 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 T0156.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 47 # # ============================================ # Comments from T0156.t2k.str.rdb # ============================================ # TARGET T0156 # 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 T0156.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 47 # # ============================================ # Comments from T0156.t2k.alpha.rdb # ============================================ # TARGET T0156 # 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 T0156.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 47 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0501 0.1330 0.8169 2 A 0.0882 0.2539 0.6579 3 I 0.0931 0.3175 0.5894 4 S 0.0748 0.3434 0.5818 5 F 0.0981 0.2551 0.6468 6 R 0.1158 0.1153 0.7689 7 P 0.1040 0.0819 0.8141 8 T 0.0719 0.5075 0.4206 9 A 0.0227 0.7737 0.2036 10 D 0.0270 0.8211 0.1519 11 L 0.0144 0.8707 0.1149 12 V 0.0147 0.8424 0.1429 13 D 0.0107 0.8480 0.1414 14 D 0.0122 0.8021 0.1857 15 I 0.0296 0.6998 0.2706 16 G 0.0223 0.5910 0.3867 17 P 0.0216 0.5713 0.4071 18 D 0.0351 0.5329 0.4320 19 V 0.0852 0.3961 0.5187 20 R 0.1377 0.2964 0.5660 21 S 0.2244 0.2993 0.4763 22 C 0.2249 0.2690 0.5061 23 D 0.1961 0.2503 0.5537 24 L 0.1989 0.2749 0.5262 25 Q 0.2512 0.2291 0.5197 26 F 0.3101 0.1399 0.5500 27 R 0.2426 0.1160 0.6414 28 Q 0.2036 0.1341 0.6623 29 F 0.1416 0.1335 0.7250 30 G 0.0965 0.1203 0.7832 31 G 0.0710 0.1174 0.8116 32 R 0.1031 0.0969 0.8001 33 S 0.3213 0.0637 0.6149 34 Q 0.5620 0.0282 0.4098 35 F 0.7011 0.0192 0.2797 36 A 0.6752 0.0195 0.3053 37 G 0.6027 0.0139 0.3835 38 P 0.6890 0.0181 0.2929 39 I 0.8256 0.0066 0.1678 40 S 0.8968 0.0052 0.0980 41 T 0.9138 0.0038 0.0825 42 V 0.8975 0.0058 0.0967 43 R 0.8692 0.0064 0.1243 44 C 0.6857 0.0114 0.3029 45 F 0.2112 0.0409 0.7479 46 Q 0.0638 0.0591 0.8772 47 D 0.0540 0.0973 0.8486 48 N 0.0487 0.2244 0.7269 49 A 0.0689 0.5758 0.3553 50 L 0.0996 0.7122 0.1882 51 L 0.0638 0.8495 0.0867 52 K 0.0553 0.8830 0.0617 53 S 0.0576 0.8809 0.0615 54 V 0.0289 0.9027 0.0683 55 L 0.0305 0.8896 0.0798 56 S 0.0310 0.8479 0.1211 57 Q 0.0465 0.6319 0.3216 58 P 0.1056 0.1291 0.7653 59 S 0.0645 0.0473 0.8882 60 A 0.0324 0.0918 0.8758 61 G 0.0399 0.0535 0.9066 62 G 0.3936 0.0127 0.5936 63 V 0.8844 0.0038 0.1118 64 L 0.9210 0.0036 0.0754 65 V 0.9191 0.0039 0.0770 66 I 0.8736 0.0101 0.1163 67 D 0.4594 0.0138 0.5268 68 G 0.0620 0.0871 0.8509 69 A 0.0463 0.0306 0.9231 70 G 0.0531 0.0462 0.9007 71 S 0.0997 0.1151 0.7853 72 L 0.2032 0.3681 0.4287 73 H 0.1270 0.4887 0.3843 74 T 0.1145 0.6422 0.2434 75 A 0.1149 0.6663 0.2188 76 L 0.1260 0.6478 0.2262 77 V 0.0332 0.8078 0.1590 78 G 0.0101 0.8871 0.1028 79 D 0.0053 0.9356 0.0590 80 V 0.0044 0.9547 0.0409 81 I 0.0044 0.9573 0.0383 82 A 0.0044 0.9576 0.0380 83 E 0.0044 0.9575 0.0380 84 L 0.0044 0.9573 0.0384 85 A 0.0044 0.9557 0.0399 86 R 0.0046 0.9465 0.0488 87 S 0.0060 0.9042 0.0898 88 T 0.0399 0.3393 0.6208 89 G 0.0380 0.0215 0.9405 90 W 0.1088 0.0135 0.8776 91 T 0.4019 0.0267 0.5714 92 G 0.8788 0.0058 0.1155 93 L 0.9274 0.0042 0.0684 94 I 0.9246 0.0061 0.0693 95 V 0.8876 0.0075 0.1049 96 H 0.4633 0.0383 0.4984 97 G 0.1586 0.0942 0.7473 98 A 0.2230 0.2074 0.5696 99 V 0.2766 0.2531 0.4703 100 R 0.2436 0.1755 0.5809 101 D 0.1419 0.1713 0.6868 102 A 0.0060 0.8928 0.1013 103 A 0.0048 0.9244 0.0708 104 A 0.0051 0.9299 0.0650 105 L 0.0075 0.9221 0.0704 106 R 0.0080 0.8667 0.1253 107 G 0.0124 0.6535 0.3341 108 I 0.0619 0.3023 0.6359 109 D 0.0467 0.0501 0.9033 110 I 0.0926 0.0348 0.8726 111 G 0.2682 0.0677 0.6641 112 I 0.5945 0.1296 0.2759 113 K 0.7010 0.1059 0.1930 114 A 0.6638 0.1004 0.2358 115 L 0.4917 0.1107 0.3976 116 G 0.3536 0.0619 0.5845 117 T 0.3581 0.0614 0.5805 118 N 0.2653 0.0497 0.6850 119 P 0.1717 0.1186 0.7098 120 R 0.1392 0.1574 0.7035 121 K 0.1602 0.1403 0.6995 122 S 0.2173 0.1253 0.6574 123 T 0.2679 0.1058 0.6263 124 K 0.2685 0.1331 0.5984 125 T 0.1809 0.1309 0.6881 126 G 0.2079 0.0858 0.7063 127 A 0.2310 0.0885 0.6805 128 G 0.3128 0.0645 0.6228 129 E 0.4110 0.0431 0.5458 130 R 0.4432 0.0231 0.5337 131 D 0.3797 0.0263 0.5940 132 V 0.4913 0.0114 0.4973 133 E 0.6648 0.0081 0.3271 134 I 0.8622 0.0082 0.1296 135 T 0.8590 0.0081 0.1330 136 L 0.6999 0.0230 0.2771 137 G 0.1581 0.0456 0.7963 138 G 0.1559 0.0482 0.7959 139 V 0.5463 0.0145 0.4392 140 T 0.7678 0.0062 0.2260 141 F 0.6869 0.0099 0.3032 142 V 0.2693 0.0158 0.7149 143 P 0.0824 0.0636 0.8540 144 G 0.0758 0.0548 0.8694 145 D 0.4688 0.0164 0.5147 146 I 0.8902 0.0038 0.1061 147 A 0.9196 0.0038 0.0766 148 Y 0.9130 0.0045 0.0825 149 S 0.8773 0.0066 0.1161 150 D 0.4898 0.0151 0.4950 151 D 0.0869 0.1222 0.7909 152 D 0.0819 0.0263 0.8917 153 G 0.2864 0.0192 0.6944 154 I 0.7119 0.0057 0.2824 155 I 0.8885 0.0038 0.1077 156 V 0.8376 0.0052 0.1572 157 V 0.1934 0.0118 0.7948