# This file is the result of combining several RDB files, specifically # T0211.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0211.t2k.stride-ebghtl.rdb (weight 1.24869) # T0211.t2k.str2.rdb (weight 1.54758) # T0211.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 T0211.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0211 # 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 T0211.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 4 # # ============================================ # Comments from T0211.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0211 # 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 T0211.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 4 # # ============================================ # Comments from T0211.t2k.str2.rdb # ============================================ # TARGET T0211 # 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 T0211.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 4 # # ============================================ # Comments from T0211.t2k.alpha.rdb # ============================================ # TARGET T0211 # 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 T0211.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 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0613 0.0332 0.9054 2 R 0.1384 0.0491 0.8125 3 K 0.2808 0.0884 0.6308 4 I 0.3849 0.0911 0.5241 5 D 0.4573 0.1054 0.4373 6 L 0.5237 0.1087 0.3675 7 C 0.4616 0.1131 0.4253 8 L 0.3662 0.1303 0.5035 9 S 0.2470 0.1169 0.6361 10 S 0.1440 0.0914 0.7646 11 E 0.0643 0.1104 0.8253 12 G 0.0864 0.0602 0.8534 13 S 0.2797 0.0188 0.7014 14 E 0.7028 0.0082 0.2890 15 V 0.9116 0.0038 0.0845 16 I 0.9238 0.0036 0.0726 17 L 0.9200 0.0036 0.0764 18 A 0.8368 0.0085 0.1547 19 T 0.5020 0.0177 0.4804 20 S 0.2028 0.0401 0.7571 21 S 0.0945 0.1150 0.7905 22 D 0.0736 0.1407 0.7857 23 E 0.0603 0.1795 0.7602 24 K 0.0721 0.1144 0.8134 25 H 0.0757 0.0482 0.8760 26 P 0.0838 0.0412 0.8751 27 P 0.0876 0.2948 0.6176 28 E 0.1339 0.3923 0.4737 29 N 0.2257 0.3723 0.4020 30 I 0.2170 0.2942 0.4888 31 I 0.2099 0.1799 0.6102 32 D 0.0995 0.0835 0.8171 33 G 0.0551 0.0712 0.8738 34 N 0.0884 0.0449 0.8668 35 P 0.0521 0.2463 0.7016 36 E 0.0605 0.3460 0.5935 37 T 0.2138 0.3593 0.4269 38 F 0.3640 0.3045 0.3315 39 W 0.4188 0.2559 0.3254 40 T 0.3746 0.2439 0.3815 41 T 0.3190 0.2151 0.4660 42 T 0.1920 0.1402 0.6678 43 G 0.1221 0.0829 0.7951 44 M 0.1848 0.0549 0.7603 45 F 0.2328 0.0493 0.7179 46 P 0.2462 0.0842 0.6696 47 Q 0.3820 0.1612 0.4568 48 E 0.6562 0.0784 0.2653 49 F 0.7831 0.0410 0.1759 50 I 0.8763 0.0145 0.1092 51 I 0.8777 0.0136 0.1087 52 C 0.8519 0.0171 0.1311 53 F 0.6763 0.0388 0.2849 54 H 0.3084 0.0800 0.6116 55 K 0.1328 0.1250 0.7421 56 H 0.2651 0.0988 0.6360 57 V 0.5749 0.0437 0.3814 58 R 0.7150 0.0286 0.2564 59 I 0.7283 0.0922 0.1795 60 E 0.6211 0.1951 0.1838 61 R 0.6667 0.2005 0.1328 62 L 0.7097 0.1870 0.1032 63 V 0.7624 0.1480 0.0897 64 I 0.7303 0.1630 0.1066 65 Q 0.6406 0.2018 0.1576 66 S 0.6344 0.1825 0.1832 67 Y 0.5927 0.2118 0.1955 68 F 0.6175 0.2153 0.1673 69 V 0.5644 0.2483 0.1873 70 Q 0.5325 0.2048 0.2627 71 T 0.5768 0.1688 0.2544 72 L 0.6507 0.1176 0.2318 73 K 0.7294 0.0802 0.1903 74 I 0.7001 0.0800 0.2199 75 E 0.5484 0.0722 0.3794 76 K 0.3695 0.0894 0.5411 77 S 0.2073 0.0987 0.6940 78 T 0.1332 0.1436 0.7233 79 S 0.1053 0.1330 0.7617 80 K 0.0680 0.2160 0.7161 81 E 0.0736 0.1557 0.7707 82 P 0.0614 0.3969 0.5417 83 V 0.0797 0.4891 0.4312 84 D 0.0887 0.5492 0.3622 85 F 0.0397 0.7655 0.1948 86 E 0.0214 0.8182 0.1604 87 Q 0.0261 0.8369 0.1371 88 W 0.0367 0.8247 0.1386 89 I 0.0681 0.7759 0.1560 90 E 0.0943 0.7326 0.1731 91 K 0.0884 0.7272 0.1844 92 D 0.1211 0.6978 0.1811 93 L 0.1668 0.5938 0.2395 94 V 0.2115 0.4780 0.3105 95 H 0.2107 0.3490 0.4404 96 T 0.1860 0.2674 0.5466 97 E 0.1535 0.1988 0.6477 98 G 0.1852 0.1176 0.6972 99 Q 0.3104 0.1070 0.5825 100 L 0.4802 0.0899 0.4299 101 Q 0.4096 0.1008 0.4897 102 N 0.3762 0.1017 0.5221 103 E 0.4312 0.0801 0.4887 104 E 0.6476 0.0348 0.3176 105 I 0.7526 0.0151 0.2322 106 V 0.6432 0.0202 0.3366 107 A 0.4458 0.0548 0.4994 108 H 0.1227 0.0823 0.7950 109 D 0.0772 0.0601 0.8626 110 G 0.1539 0.0718 0.7744 111 S 0.2565 0.0998 0.6437 112 A 0.4838 0.0790 0.4372 113 T 0.6390 0.1047 0.2563 114 Y 0.7989 0.0478 0.1533 115 L 0.8036 0.0401 0.1563 116 R 0.8483 0.0348 0.1169 117 F 0.8982 0.0259 0.0758 118 I 0.8761 0.0406 0.0833 119 I 0.8206 0.0738 0.1056 120 V 0.7016 0.0960 0.2025 121 S 0.3903 0.0897 0.5199 122 A 0.1517 0.2251 0.6231 123 F 0.1208 0.3078 0.5714 124 D 0.1170 0.3308 0.5522 125 H 0.2441 0.1947 0.5612 126 F 0.4000 0.1110 0.4890 127 A 0.5290 0.0679 0.4031 128 S 0.6514 0.0391 0.3095 129 V 0.6727 0.0433 0.2840 130 H 0.7138 0.0449 0.2413 131 S 0.7560 0.0274 0.2166 132 V 0.7983 0.0220 0.1798 133 S 0.7511 0.0234 0.2255 134 A 0.6160 0.0830 0.3010 135 E 0.3849 0.0976 0.5174 136 G 0.3513 0.1061 0.5426 137 T 0.6065 0.0836 0.3100 138 V 0.7121 0.0720 0.2158 139 V 0.6317 0.1080 0.2603 140 S 0.4534 0.1535 0.3930 141 N 0.3192 0.1553 0.5255 142 L 0.2069 0.1282 0.6648 143 S 0.1159 0.0832 0.8009 144 S 0.0386 0.0434 0.9179