# This file is the result of combining several RDB files, specifically # T0265.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0265.t2k.stride-ebghtl.rdb (weight 1.24869) # T0265.t2k.str2.rdb (weight 1.54758) # T0265.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 T0265.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0265 # 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 T0265.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 269 # # ============================================ # Comments from T0265.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0265 # 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 T0265.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 269 # # ============================================ # Comments from T0265.t2k.str2.rdb # ============================================ # TARGET T0265 # 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 T0265.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 269 # # ============================================ # Comments from T0265.t2k.alpha.rdb # ============================================ # TARGET T0265 # 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 T0265.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 269 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0277 0.4135 0.5587 2 M 0.0412 0.7570 0.2019 3 K 0.0292 0.7768 0.1940 4 E 0.0282 0.8142 0.1576 5 K 0.0291 0.8218 0.1491 6 L 0.0353 0.8195 0.1452 7 E 0.0388 0.7906 0.1706 8 S 0.0361 0.7728 0.1911 9 K 0.0305 0.8028 0.1667 10 K 0.0211 0.8023 0.1766 11 D 0.0157 0.8104 0.1739 12 E 0.0122 0.8535 0.1343 13 I 0.0145 0.8762 0.1093 14 R 0.0154 0.8534 0.1312 15 C 0.0215 0.7854 0.1932 16 C 0.0280 0.6747 0.2973 17 Y 0.0562 0.3305 0.6133 18 K 0.0491 0.0534 0.8975 19 I 0.0701 0.0191 0.9108 20 T 0.0522 0.0197 0.9281 21 D 0.0062 0.8830 0.1108 22 T 0.0052 0.9236 0.0712 23 D 0.0049 0.9513 0.0439 24 V 0.0047 0.9599 0.0354 25 A 0.0047 0.9602 0.0352 26 V 0.0047 0.9605 0.0349 27 L 0.0050 0.9599 0.0351 28 L 0.0047 0.9597 0.0356 29 K 0.0047 0.9579 0.0374 30 M 0.0049 0.9472 0.0479 31 V 0.0070 0.9038 0.0892 32 E 0.0104 0.7769 0.2127 33 I 0.0347 0.5074 0.4579 34 E 0.0425 0.1151 0.8424 35 K 0.0476 0.0788 0.8735 36 P 0.0936 0.0645 0.8418 37 I 0.2462 0.0241 0.7297 38 T 0.1987 0.0184 0.7829 39 S 0.0062 0.9219 0.0718 40 E 0.0047 0.9484 0.0469 41 E 0.0048 0.9542 0.0410 42 L 0.0047 0.9554 0.0398 43 A 0.0048 0.9506 0.0446 44 D 0.0053 0.9296 0.0651 45 I 0.0064 0.8801 0.1135 46 F 0.0526 0.4878 0.4595 47 K 0.0438 0.0599 0.8963 48 L 0.0703 0.0261 0.9036 49 S 0.0583 0.0147 0.9270 50 K 0.0117 0.8545 0.1338 51 T 0.0052 0.9228 0.0720 52 T 0.0055 0.9398 0.0547 53 V 0.0048 0.9530 0.0422 54 E 0.0047 0.9561 0.0392 55 N 0.0047 0.9564 0.0389 56 S 0.0047 0.9574 0.0379 57 L 0.0047 0.9585 0.0368 58 K 0.0048 0.9592 0.0361 59 K 0.0048 0.9584 0.0368 60 L 0.0048 0.9559 0.0393 61 I 0.0054 0.9404 0.0541 62 E 0.0053 0.8690 0.1257 63 L 0.0429 0.2418 0.7152 64 G 0.0351 0.0243 0.9406 65 L 0.1876 0.0319 0.7804 66 V 0.7892 0.0125 0.1983 67 V 0.8525 0.0146 0.1329 68 R 0.8598 0.0117 0.1284 69 T 0.8315 0.0095 0.1590 70 K 0.7390 0.0188 0.2422 71 T 0.3845 0.0315 0.5841 72 E 0.1387 0.1529 0.7085 73 G 0.0658 0.1604 0.7737 74 K 0.0955 0.1371 0.7674 75 K 0.1254 0.1019 0.7727 76 I 0.3049 0.0659 0.6291 77 G 0.5354 0.0296 0.4350 78 R 0.6655 0.0163 0.3183 79 P 0.7763 0.0135 0.2101 80 K 0.7989 0.0211 0.1800 81 Y 0.8046 0.0213 0.1741 82 Y 0.7302 0.0494 0.2204 83 Y 0.5390 0.0829 0.3782 84 S 0.3398 0.2411 0.4192 85 I 0.1005 0.3454 0.5541 86 S 0.0626 0.4291 0.5083 87 S 0.0276 0.6863 0.2861 88 N 0.0242 0.7674 0.2084 89 I 0.0140 0.8343 0.1517 90 L 0.0075 0.8896 0.1029 91 E 0.0063 0.9026 0.0911 92 K 0.0068 0.8986 0.0946 93 I 0.0071 0.9055 0.0874 94 R 0.0053 0.9422 0.0525 95 N 0.0053 0.9452 0.0495 96 D 0.0052 0.9483 0.0465 97 L 0.0050 0.9509 0.0440 98 L 0.0049 0.9507 0.0444 99 N 0.0050 0.9458 0.0491 100 C 0.0049 0.9469 0.0482 101 A 0.0048 0.9505 0.0447 102 K 0.0048 0.9464 0.0488 103 R 0.0049 0.9415 0.0536 104 M 0.0049 0.9356 0.0595 105 E 0.0053 0.9046 0.0901 106 L 0.0078 0.8191 0.1732 107 A 0.0142 0.6303 0.3555 108 A 0.0587 0.2731 0.6681 109 T 0.0440 0.0727 0.8833