# This file is the result of combining several RDB files, specifically # T0262.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0262.t2k.stride-ebghtl.rdb (weight 1.24869) # T0262.t2k.str2.rdb (weight 1.54758) # T0262.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 T0262.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 2 # # ============================================ # Comments from T0262.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 2 # # ============================================ # Comments from T0262.t2k.str2.rdb # ============================================ # TARGET T0262 # 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 T0262.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 2 # # ============================================ # Comments from T0262.t2k.alpha.rdb # ============================================ # TARGET T0262 # 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 T0262.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0568 0.0307 0.9126 2 P 0.0755 0.0641 0.8604 3 S 0.0777 0.1433 0.7790 4 S 0.0561 0.2988 0.6451 5 S 0.0726 0.3927 0.5347 6 Q 0.0982 0.4476 0.4542 7 Y 0.1492 0.4299 0.4208 8 R 0.1619 0.3964 0.4417 9 R 0.1588 0.3875 0.4537 10 Y 0.1348 0.2762 0.5890 11 Q 0.1273 0.1716 0.7010 12 D 0.0995 0.0725 0.8280 13 P 0.0415 0.1506 0.8078 14 H 0.0609 0.1155 0.8236 15 H 0.0973 0.0716 0.8311 16 P 0.0747 0.1158 0.8096 17 S 0.0958 0.1041 0.8002 18 I 0.1346 0.0423 0.8231 19 P 0.1291 0.0416 0.8293 20 T 0.1266 0.0394 0.8340 21 P 0.1332 0.1269 0.7399 22 T 0.1786 0.1809 0.6405 23 T 0.3069 0.2152 0.4779 24 L 0.3386 0.2140 0.4474 25 F 0.2940 0.1754 0.5306 26 S 0.2488 0.1381 0.6130 27 Q 0.1707 0.1082 0.7211 28 P 0.1463 0.2024 0.6513 29 S 0.2407 0.2664 0.4929 30 L 0.2984 0.3468 0.3548 31 E 0.3526 0.3527 0.2948 32 I 0.3390 0.3395 0.3215 33 L 0.2221 0.2657 0.5122 34 G 0.1020 0.1962 0.7017 35 G 0.0639 0.1981 0.7380 36 G 0.0764 0.3077 0.6159 37 V 0.0527 0.6530 0.2943 38 A 0.0221 0.8004 0.1775 39 E 0.0243 0.7558 0.2199 40 E 0.0342 0.6911 0.2747 41 L 0.0656 0.5326 0.4018 42 P 0.0513 0.6454 0.3033 43 E 0.0732 0.6894 0.2374 44 L 0.1206 0.6955 0.1839 45 A 0.2026 0.5944 0.2030 46 L 0.2661 0.4627 0.2712 47 C 0.2770 0.3237 0.3994 48 C 0.2058 0.1834 0.6108 49 D 0.0814 0.0776 0.8410 50 G 0.1028 0.0848 0.8124 51 T 0.4702 0.0414 0.4884 52 V 0.6670 0.0374 0.2956 53 V 0.5700 0.0519 0.3781 54 E 0.3584 0.0751 0.5665 55 G 0.1678 0.0724 0.7599 56 R 0.1707 0.0846 0.7447 57 S 0.1681 0.1418 0.6900 58 N 0.1835 0.1446 0.6718 59 C 0.2642 0.1558 0.5800 60 R 0.4215 0.1485 0.4300 61 C 0.5638 0.1340 0.3022 62 K 0.5690 0.1286 0.3024 63 A 0.5709 0.1541 0.2750 64 R 0.5950 0.1424 0.2627 65 A 0.6365 0.1091 0.2544 66 V 0.6659 0.0702 0.2640 67 L 0.4600 0.0403 0.4997 68 P 0.1860 0.0812 0.7328 69 G 0.1109 0.0720 0.8171 70 G 0.2316 0.0634 0.7049 71 M 0.5264 0.0382 0.4354 72 R 0.7903 0.0285 0.1812 73 V 0.7914 0.0410 0.1676 74 R 0.7297 0.0541 0.2162 75 L 0.5034 0.1695 0.3271 76 S 0.2767 0.3154 0.4080 77 K 0.1687 0.4512 0.3801 78 T 0.1388 0.5108 0.3503 79 L 0.1142 0.6257 0.2601 80 A 0.0834 0.6553 0.2614 81 G 0.0796 0.6378 0.2826 82 I 0.1102 0.5930 0.2967 83 L 0.1359 0.4455 0.4187 84 R 0.0999 0.2377 0.6624 85 H 0.0453 0.0405 0.9142