# This file is the result of combining several RDB files, specifically # T0222.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0222.t2k.stride-ebghtl.rdb (weight 1.24869) # T0222.t2k.str2.rdb (weight 1.54758) # T0222.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 T0222.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 76 # # ============================================ # Comments from T0222.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 76 # # ============================================ # Comments from T0222.t2k.str2.rdb # ============================================ # TARGET T0222 # 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 T0222.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 76 # # ============================================ # Comments from T0222.t2k.alpha.rdb # ============================================ # TARGET T0222 # 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 T0222.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 76 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.2246 0.0255 0.7499 2 F 0.4650 0.0231 0.5119 3 T 0.4721 0.0274 0.5005 4 I 0.4025 0.0614 0.5360 5 D 0.2804 0.0520 0.6676 6 K 0.1062 0.1606 0.7332 7 N 0.0760 0.1091 0.8149 8 L 0.0935 0.0650 0.8415 9 P 0.0909 0.0645 0.8446 10 G 0.0956 0.0423 0.8622 11 A 0.0988 0.0917 0.8094 12 D 0.1036 0.1287 0.7677 13 H 0.1106 0.2710 0.6184 14 S 0.2144 0.3086 0.4771 15 F 0.2450 0.2726 0.4824 16 A 0.2503 0.1897 0.5600 17 L 0.1773 0.1215 0.7012 18 N 0.0902 0.0477 0.8621 19 P 0.0084 0.8859 0.1057 20 D 0.0051 0.9323 0.0626 21 E 0.0052 0.9404 0.0543 22 L 0.0047 0.9560 0.0393 23 K 0.0047 0.9588 0.0365 24 E 0.0047 0.9580 0.0372 25 M 0.0047 0.9569 0.0383 26 V 0.0047 0.9591 0.0362 27 D 0.0047 0.9579 0.0374 28 G 0.0047 0.9558 0.0395 29 I 0.0047 0.9586 0.0367 30 R 0.0047 0.9589 0.0364 31 K 0.0047 0.9583 0.0370 32 T 0.0047 0.9575 0.0378 33 E 0.0049 0.9525 0.0426 34 A 0.0055 0.9363 0.0581 35 E 0.0097 0.8759 0.1144 36 L 0.0405 0.6212 0.3382 37 K 0.0354 0.1750 0.7896 38 Q 0.0471 0.1633 0.7896 39 G 0.0614 0.2228 0.7157 40 I 0.1435 0.2161 0.6404 41 T 0.1657 0.2942 0.5401 42 K 0.1469 0.3538 0.4993 43 P 0.0960 0.7188 0.1852 44 V 0.0598 0.8042 0.1360 45 S 0.0456 0.8364 0.1180 46 E 0.0402 0.8263 0.1335 47 K 0.0387 0.7978 0.1635 48 L 0.0606 0.6990 0.2403 49 L 0.0746 0.4856 0.4398 50 G 0.0582 0.2350 0.7068 51 S 0.0602 0.1335 0.8062 52 S 0.0544 0.1520 0.7936 53 Y 0.1206 0.2151 0.6643 54 K 0.1685 0.2502 0.5813 55 T 0.2197 0.2000 0.5803 56 T 0.1494 0.1480 0.7026 57 T 0.0866 0.0779 0.8355 58 A 0.0231 0.5349 0.4420 59 I 0.0300 0.6238 0.3462 60 E 0.0243 0.6993 0.2764 61 G 0.0312 0.7391 0.2297 62 E 0.0362 0.7359 0.2279 63 I 0.0460 0.6952 0.2588 64 R 0.0435 0.7431 0.2134 65 N 0.0475 0.7543 0.1982 66 F 0.0535 0.7391 0.2074 67 A 0.0650 0.6912 0.2438 68 Y 0.1000 0.6032 0.2968 69 R 0.1904 0.5147 0.2949 70 G 0.3208 0.4331 0.2461 71 I 0.5337 0.3096 0.1567 72 F 0.6361 0.2412 0.1228 73 T 0.6289 0.2154 0.1557 74 T 0.6371 0.1730 0.1900 75 A 0.5874 0.1363 0.2764 76 P 0.5306 0.1238 0.3456 77 I 0.2959 0.1015 0.6026 78 Q 0.1607 0.1024 0.7369 79 K 0.0519 0.1323 0.8158 80 G 0.0693 0.0614 0.8693 81 E 0.3818 0.0314 0.5868 82 A 0.7451 0.0184 0.2366 83 F 0.6424 0.0224 0.3352 84 S 0.3913 0.0223 0.5864 85 E 0.0498 0.6091 0.3411 86 D 0.0341 0.5489 0.4171 87 N 0.1197 0.5355 0.3448 88 I 0.5742 0.0474 0.3784 89 A 0.8133 0.0452 0.1415 90 V 0.8657 0.0220 0.1124 91 L 0.7847 0.0247 0.1907 92 R 0.4096 0.0344 0.5561 93 P 0.0627 0.1667 0.7706 94 G 0.0322 0.1516 0.8162 95 Q 0.0919 0.1518 0.7563 96 K 0.1123 0.0727 0.8150 97 P 0.0809 0.1391 0.7801 98 Q 0.0439 0.1433 0.8128 99 G 0.0642 0.1095 0.8263 100 L 0.1208 0.0695 0.8097 101 H 0.1003 0.0857 0.8140 102 P 0.0357 0.6645 0.2998 103 R 0.0207 0.7545 0.2248 104 F 0.0286 0.7367 0.2347 105 F 0.0209 0.8781 0.1010 106 E 0.0136 0.8858 0.1006 107 L 0.0167 0.8788 0.1044 108 L 0.0258 0.8627 0.1115 109 T 0.0463 0.7658 0.1879 110 S 0.0563 0.5356 0.4082 111 G 0.0479 0.2639 0.6881 112 V 0.1485 0.2714 0.5800 113 R 0.3501 0.3058 0.3441 114 A 0.2698 0.3696 0.3606 115 V 0.2937 0.3928 0.3134 116 R 0.2599 0.3744 0.3657 117 D 0.2355 0.2857 0.4788 118 I 0.1612 0.1119 0.7269 119 P 0.0921 0.0712 0.8367 120 A 0.0292 0.1052 0.8656 121 D 0.0210 0.0463 0.9327 122 T 0.0992 0.0283 0.8725 123 G 0.2920 0.0183 0.6896 124 I 0.4913 0.0153 0.4934 125 V 0.2805 0.0172 0.7023 126 W 0.0370 0.6323 0.3308 127 D 0.0248 0.6700 0.3051 128 D 0.0393 0.7102 0.2505 129 I 0.1724 0.4978 0.3298 130 L 0.3182 0.3303 0.3515 131 L 0.1752 0.2658 0.5589 132 K 0.0470 0.1737 0.7793 133 D 0.0430 0.0740 0.8830 134 S 0.0837 0.0429 0.8734 135 P 0.0816 0.1677 0.7507 136 F 0.1207 0.1868 0.6926 137 H 0.1176 0.1512 0.7312 138 E 0.0378 0.0573 0.9048