# This file is the result of combining several RDB files, specifically # T0344.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0344.t2k.stride-ebghtl.rdb (weight 1.24869) # T0344.t2k.str2.rdb (weight 1.54758) # T0344.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 T0344.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 T0344.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 T0344.t2k.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 T0344.t2k.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 0.1082 0.0160 0.8757 2 R 0.4150 0.0183 0.5667 3 I 0.7856 0.0157 0.1986 4 V 0.8308 0.0292 0.1400 5 A 0.8137 0.0191 0.1672 6 A 0.6719 0.0511 0.2770 7 D 0.4119 0.0576 0.5304 8 T 0.1837 0.0949 0.7214 9 G 0.1219 0.0891 0.7890 10 G 0.1574 0.1431 0.6995 11 A 0.2888 0.1610 0.5502 12 V 0.4816 0.1686 0.3497 13 L 0.4753 0.1639 0.3608 14 D 0.2900 0.1694 0.5406 15 E 0.0924 0.2987 0.6089 16 T 0.0500 0.2448 0.7052 17 F 0.0789 0.1849 0.7362 18 E 0.0994 0.1162 0.7844 19 P 0.2047 0.2092 0.5861 20 I 0.3708 0.2598 0.3694 21 G 0.4837 0.2379 0.2784 22 L 0.6095 0.2559 0.1346 23 I 0.5899 0.3024 0.1077 24 A 0.6156 0.2710 0.1134 25 T 0.6616 0.2241 0.1142 26 V 0.6340 0.2342 0.1318 27 A 0.5808 0.2888 0.1304 28 V 0.5908 0.2796 0.1297 29 L 0.6042 0.2254 0.1704 30 V 0.5279 0.1674 0.3047 31 E 0.3810 0.0925 0.5266 32 K 0.2346 0.0585 0.7069 33 P 0.1713 0.1156 0.7131 34 Y 0.1176 0.1928 0.6896 35 R 0.1402 0.1832 0.6766 36 S 0.1736 0.1730 0.6534 37 A 0.1476 0.3163 0.5361 38 K 0.2287 0.2996 0.4717 39 E 0.4284 0.2041 0.3676 40 V 0.5337 0.1221 0.3441 41 M 0.7008 0.0765 0.2227 42 V 0.7696 0.0591 0.1713 43 K 0.7209 0.0842 0.1949 44 Y 0.5912 0.0666 0.3421 45 A 0.2830 0.0573 0.6598 46 N 0.1386 0.0325 0.8289 47 P 0.0679 0.1799 0.7522 48 Y 0.1016 0.1698 0.7286 49 D 0.1571 0.1441 0.6988 50 Y 0.1428 0.1470 0.7101 51 D 0.1225 0.1489 0.7286 52 L 0.0654 0.2528 0.6818 53 T 0.0551 0.2663 0.6786 54 G 0.0390 0.4599 0.5011 55 R 0.0381 0.6708 0.2911 56 Q 0.0520 0.7555 0.1925 57 A 0.0419 0.7969 0.1613 58 I 0.0255 0.8632 0.1113 59 R 0.0185 0.8835 0.0980 60 D 0.0122 0.8953 0.0924 61 E 0.0077 0.9423 0.0500 62 V 0.0059 0.9546 0.0395 63 L 0.0060 0.9562 0.0378 64 L 0.0065 0.9550 0.0385 65 A 0.0050 0.9554 0.0396 66 I 0.0069 0.9519 0.0412 67 E 0.0085 0.9393 0.0522 68 L 0.0114 0.9097 0.0789 69 A 0.0075 0.9021 0.0904 70 R 0.0130 0.8133 0.1738 71 K 0.0338 0.6099 0.3563 72 V 0.1130 0.2453 0.6417 73 K 0.0776 0.0471 0.8753 74 P 0.0814 0.0697 0.8490 75 D 0.1068 0.1075 0.7857 76 V 0.6631 0.0465 0.2904 77 I 0.8457 0.0197 0.1346 78 H 0.8315 0.0127 0.1558 79 L 0.7033 0.0414 0.2554 80 D 0.3694 0.0624 0.5682 81 S 0.2229 0.1084 0.6687 82 T 0.1951 0.1268 0.6781 83 L 0.1314 0.1508 0.7178 84 G 0.0989 0.0902 0.8109 85 G 0.1997 0.0899 0.7104 86 I 0.5226 0.0873 0.3902 87 E 0.6315 0.1036 0.2649 88 L 0.6217 0.1176 0.2607 89 R 0.5081 0.1781 0.3138 90 K 0.4058 0.1900 0.4042 91 L 0.2704 0.1943 0.5353 92 D 0.1154 0.1454 0.7392 93 E 0.0813 0.2423 0.6764 94 P 0.0817 0.3701 0.5482 95 T 0.0971 0.5225 0.3804 96 I 0.0423 0.7454 0.2124 97 D 0.0463 0.7486 0.2050 98 A 0.0452 0.7295 0.2253 99 L 0.1031 0.4513 0.4455 100 G 0.1400 0.2627 0.5973 101 I 0.1742 0.2228 0.6030 102 S 0.1406 0.1943 0.6650 103 D 0.0397 0.4361 0.5242 104 K 0.0334 0.4444 0.5222 105 G 0.0298 0.3942 0.5759 106 K 0.1192 0.5178 0.3630 107 E 0.1891 0.5992 0.2117 108 V 0.0911 0.7287 0.1803 109 W 0.0365 0.8186 0.1449 110 K 0.0183 0.8474 0.1343 111 E 0.0192 0.8048 0.1760 112 L 0.0265 0.7526 0.2210 113 S 0.0249 0.6512 0.3239 114 K 0.0131 0.5983 0.3885 115 D 0.0236 0.5308 0.4456 116 L 0.0202 0.6923 0.2874 117 Q 0.0099 0.7778 0.2123 118 P 0.0057 0.8895 0.1047 119 L 0.0049 0.9201 0.0750 120 A 0.0049 0.9340 0.0611 121 R 0.0051 0.9305 0.0644 122 K 0.0058 0.9259 0.0683 123 F 0.0081 0.9148 0.0771 124 W 0.0150 0.8821 0.1029 125 E 0.0132 0.8800 0.1068 126 E 0.0270 0.7662 0.2068 127 T 0.0567 0.4360 0.5073 128 N 0.0500 0.0406 0.9094 129 I 0.1854 0.0202 0.7944 130 E 0.6149 0.0082 0.3769 131 I 0.8488 0.0076 0.1436 132 V 0.8924 0.0086 0.0990 133 A 0.8615 0.0105 0.1280 134 I 0.7147 0.0355 0.2498 135 G 0.4925 0.0288 0.4786 136 K 0.2173 0.0886 0.6940 137 S 0.1655 0.1168 0.7177 138 S 0.1856 0.1026 0.7118 139 V 0.2323 0.0774 0.6904 140 P 0.4413 0.1161 0.4426 141 V 0.5418 0.2057 0.2526 142 R 0.6616 0.2124 0.1260 143 I 0.6079 0.3015 0.0906 144 A 0.6105 0.3023 0.0873 145 E 0.5748 0.3283 0.0968 146 I 0.4371 0.4208 0.1421 147 Y 0.2663 0.5216 0.2120 148 A 0.1365 0.5970 0.2666 149 G 0.1123 0.5846 0.3031 150 I 0.0920 0.7406 0.1674 151 Y 0.0960 0.7693 0.1347 152 S 0.0725 0.8073 0.1202 153 A 0.0495 0.8607 0.0898 154 K 0.0277 0.9010 0.0713 155 W 0.0355 0.8847 0.0798 156 G 0.0393 0.8592 0.1015 157 I 0.0301 0.8708 0.0991 158 E 0.0387 0.8464 0.1149 159 N 0.0433 0.7998 0.1570 160 V 0.1513 0.6415 0.2072 161 E 0.1644 0.5821 0.2535 162 K 0.1366 0.5105 0.3529 163 E 0.0895 0.1286 0.7820 164 G 0.0411 0.0326 0.9264 165 H 0.3562 0.0214 0.6224 166 L 0.8607 0.0054 0.1340 167 I 0.8942 0.0073 0.0984 168 I 0.8436 0.0269 0.1294 169 G 0.6539 0.0145 0.3316 170 L 0.2432 0.0289 0.7280 171 P 0.1312 0.1353 0.7335 172 R 0.1215 0.2426 0.6359 173 Y 0.2058 0.2605 0.5337 174 M 0.2485 0.1430 0.6085 175 E 0.1971 0.0678 0.7351 176 V 0.0592 0.0281 0.9128