# This file is the result of combining several RDB files, specifically # T0272.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0272.t2k.stride-ebghtl.rdb (weight 1.24869) # T0272.t2k.str2.rdb (weight 1.54758) # T0272.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 T0272.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 11 # # ============================================ # Comments from T0272.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 11 # # ============================================ # Comments from T0272.t2k.str2.rdb # ============================================ # TARGET T0272 # 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 T0272.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 11 # # ============================================ # Comments from T0272.t2k.alpha.rdb # ============================================ # TARGET T0272 # 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 T0272.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 11 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2043 0.0148 0.7809 2 W 0.5898 0.0240 0.3862 3 L 0.6988 0.0275 0.2737 4 T 0.7056 0.0397 0.2547 5 K 0.7651 0.0234 0.2115 6 L 0.8266 0.0150 0.1584 7 V 0.7984 0.0140 0.1876 8 L 0.5498 0.0203 0.4299 9 N 0.1555 0.0155 0.8290 10 P 0.0279 0.3273 0.6448 11 A 0.0260 0.4634 0.5106 12 S 0.0249 0.6745 0.3005 13 R 0.0146 0.8467 0.1387 14 A 0.0164 0.8633 0.1202 15 A 0.0187 0.8663 0.1150 16 R 0.0229 0.8586 0.1185 17 R 0.0271 0.8197 0.1531 18 D 0.0269 0.7257 0.2474 19 L 0.0312 0.5373 0.4315 20 A 0.0379 0.3090 0.6532 21 N 0.0466 0.1608 0.7925 22 P 0.0344 0.5105 0.4551 23 Y 0.0299 0.7406 0.2295 24 E 0.0151 0.8793 0.1056 25 M 0.0103 0.9036 0.0861 26 H 0.0114 0.9216 0.0671 27 R 0.0152 0.9292 0.0556 28 T 0.0117 0.9345 0.0538 29 L 0.0079 0.9329 0.0592 30 S 0.0079 0.9082 0.0840 31 K 0.0091 0.8116 0.1794 32 A 0.0161 0.6497 0.3343 33 V 0.0743 0.1579 0.7677 34 S 0.0312 0.1743 0.7945 35 R 0.0373 0.1100 0.8528 36 A 0.0717 0.1442 0.7841 37 L 0.0163 0.5107 0.4730 38 E 0.0169 0.5253 0.4578 39 E 0.0361 0.4941 0.4698 40 G 0.0577 0.3642 0.5781 41 R 0.0547 0.2954 0.6500 42 E 0.0596 0.1834 0.7570 43 R 0.1401 0.1133 0.7466 44 L 0.4108 0.0643 0.5249 45 L 0.6245 0.0648 0.3106 46 W 0.7054 0.0479 0.2468 47 R 0.6690 0.0437 0.2873 48 L 0.5241 0.0587 0.4172 49 E 0.2686 0.0648 0.6666 50 P 0.1875 0.0968 0.7157 51 A 0.0907 0.2311 0.6782 52 R 0.0705 0.2224 0.7071 53 G 0.0839 0.2195 0.6966 54 L 0.0798 0.1553 0.7650 55 E 0.1175 0.0805 0.8020 56 P 0.1797 0.0281 0.7921 57 P 0.4142 0.0109 0.5749 58 V 0.8528 0.0050 0.1423 59 V 0.9261 0.0033 0.0705 60 L 0.9241 0.0036 0.0723 61 V 0.9264 0.0031 0.0705 62 Q 0.8467 0.0086 0.1446 63 T 0.4778 0.0106 0.5116 64 L 0.1884 0.0758 0.7357 65 T 0.1133 0.0883 0.7984 66 E 0.1062 0.0845 0.8093 67 P 0.1028 0.1113 0.7860 68 D 0.1309 0.1920 0.6771 69 W 0.1140 0.3822 0.5038 70 S 0.1179 0.4240 0.4581 71 V 0.1127 0.4299 0.4573 72 L 0.1067 0.3337 0.5596 73 D 0.0784 0.2651 0.6565 74 E 0.0777 0.1846 0.7378 75 G 0.1487 0.0978 0.7535 76 Y 0.2522 0.0824 0.6654 77 A 0.5624 0.0577 0.3799 78 Q 0.7315 0.0304 0.2381 79 V 0.7794 0.0215 0.1991 80 F 0.6383 0.0195 0.3421 81 P 0.4231 0.0229 0.5540 82 P 0.2840 0.0445 0.6714 83 K 0.2851 0.0406 0.6743 84 P 0.2001 0.0729 0.7269 85 F 0.1704 0.0828 0.7468 86 H 0.1291 0.1498 0.7211 87 P 0.0838 0.2953 0.6209 88 A 0.1419 0.2416 0.6165 89 L 0.2699 0.0716 0.6585 90 K 0.0985 0.0298 0.8718 91 P 0.0289 0.0772 0.8939 92 G 0.0290 0.0448 0.9263 93 Q 0.2720 0.0159 0.7121 94 R 0.7655 0.0041 0.2304 95 L 0.8934 0.0045 0.1021 96 R 0.9157 0.0034 0.0809 97 F 0.9075 0.0039 0.0887 98 R 0.9000 0.0049 0.0952 99 L 0.8753 0.0057 0.1190 100 R 0.8019 0.0110 0.1870 101 A 0.6478 0.0144 0.3379 102 N 0.2718 0.0196 0.7086 103 P 0.1817 0.1318 0.6865 104 A 0.3531 0.1334 0.5134 105 K 0.4618 0.1164 0.4218 106 R 0.3608 0.1038 0.5354 107 L 0.2031 0.2490 0.5479 108 A 0.1240 0.2097 0.6662 109 A 0.0941 0.1843 0.7216 110 T 0.0915 0.1080 0.8005 111 G 0.0438 0.0539 0.9023