# This file is the result of combining several RDB files, specifically # T0289.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0289.t2k.stride-ebghtl.rdb (weight 1.24869) # T0289.t2k.str2.rdb (weight 1.54758) # T0289.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 T0289.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 46 # # ============================================ # Comments from T0289.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 46 # # ============================================ # Comments from T0289.t2k.str2.rdb # ============================================ # TARGET T0289 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0289.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 11.2611 # # ============================================ # Comments from T0289.t2k.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 46 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0787 0.0243 0.8970 2 P 0.1022 0.0701 0.8277 3 C 0.1243 0.1118 0.7639 4 A 0.4014 0.0920 0.5066 5 I 0.7291 0.0198 0.2510 6 D 0.8540 0.0167 0.1292 7 V 0.8922 0.0124 0.0954 8 Y 0.8642 0.0232 0.1126 9 K 0.8141 0.0325 0.1533 10 I 0.6527 0.0573 0.2900 11 M 0.4370 0.1027 0.4603 12 E 0.3530 0.1144 0.5326 13 K 0.3785 0.0715 0.5501 14 V 0.4401 0.0233 0.5367 15 D 0.3804 0.0222 0.5974 16 Y 0.3883 0.0160 0.5957 17 P 0.3593 0.0204 0.6203 18 R 0.4874 0.0316 0.4810 19 N 0.1313 0.0246 0.8441 20 E 0.0262 0.1174 0.8564 21 S 0.0485 0.0193 0.9322 22 G 0.0473 0.0251 0.9275 23 D 0.2406 0.0119 0.7475 24 V 0.7985 0.0040 0.1976 25 A 0.8310 0.0150 0.1540 26 A 0.8950 0.0075 0.0975 27 V 0.8978 0.0111 0.0911 28 I 0.8435 0.0106 0.1460 29 H 0.5415 0.0158 0.4427 30 P 0.1251 0.3259 0.5490 31 N 0.0712 0.3523 0.5764 32 L 0.1074 0.3514 0.5411 33 Q 0.1487 0.1647 0.6866 34 D 0.0914 0.1388 0.7699 35 Q 0.0949 0.1547 0.7505 36 D 0.1517 0.1245 0.7238 37 W 0.2151 0.2146 0.5703 38 K 0.2430 0.1422 0.6148 39 P 0.3661 0.1039 0.5300 40 L 0.2668 0.0641 0.6691 41 H 0.0845 0.0285 0.8869 42 P 0.0286 0.0673 0.9041 43 G 0.0210 0.0413 0.9377 44 D 0.0930 0.0205 0.8865 45 P 0.3844 0.0270 0.5886 46 V 0.6262 0.0609 0.3129 47 F 0.7706 0.0400 0.1894 48 V 0.8013 0.0256 0.1731 49 S 0.6079 0.0337 0.3584 50 L 0.3224 0.0710 0.6066 51 D 0.0802 0.0389 0.8809 52 G 0.0578 0.0510 0.8912 53 K 0.3661 0.0224 0.6114 54 V 0.7996 0.0084 0.1920 55 I 0.7902 0.0093 0.2004 56 P 0.7322 0.0148 0.2531 57 L 0.4765 0.0469 0.4766 58 G 0.1564 0.0741 0.7695 59 G 0.0724 0.0698 0.8578 60 D 0.1116 0.0663 0.8221 61 C 0.2111 0.0390 0.7499 62 T 0.4239 0.0300 0.5460 63 V 0.6197 0.0253 0.3550 64 Y 0.6415 0.0213 0.3372 65 P 0.6853 0.0384 0.2763 66 V 0.8068 0.0597 0.1335 67 F 0.8098 0.0698 0.1204 68 V 0.6486 0.1751 0.1763 69 N 0.3872 0.2573 0.3555 70 E 0.1707 0.5248 0.3045 71 A 0.0987 0.7265 0.1749 72 A 0.0942 0.7629 0.1429 73 Y 0.0995 0.7635 0.1370 74 Y 0.1108 0.7303 0.1589 75 E 0.0991 0.6985 0.2023 76 K 0.0525 0.5522 0.3953 77 K 0.0466 0.3856 0.5677 78 E 0.1384 0.4386 0.4230 79 A 0.2963 0.4034 0.3003 80 F 0.3832 0.3498 0.2670 81 A 0.5343 0.2458 0.2199 82 K 0.5247 0.2153 0.2600 83 T 0.5899 0.1087 0.3014 84 T 0.6037 0.0747 0.3216 85 K 0.6415 0.0592 0.2994 86 L 0.7123 0.0488 0.2389 87 T 0.7286 0.0390 0.2324 88 L 0.7140 0.0232 0.2628 89 N 0.6346 0.0310 0.3344 90 A 0.3767 0.2372 0.3860 91 K 0.2296 0.3730 0.3974 92 S 0.3033 0.4303 0.2665 93 I 0.3867 0.4066 0.2066 94 R 0.3834 0.3449 0.2717 95 S 0.2859 0.3096 0.4045 96 T 0.2087 0.2248 0.5665 97 L 0.1435 0.1478 0.7087 98 H 0.0601 0.0463 0.8937