# This file is the result of combining several RDB files, specifically # T0187.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0187.t2k.stride-ebghtl.rdb (weight 1.24869) # T0187.t2k.str.rdb (weight 1.53983) # T0187.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 T0187.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ # Comments from T0187.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ # Comments from T0187.t2k.str.rdb # ============================================ # TARGET T0187 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0187.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 29 # # ============================================ # Comments from T0187.t2k.alpha.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0672 0.0257 0.9071 2 K 0.0902 0.0227 0.8870 3 K 0.0977 0.0243 0.8780 4 P 0.3498 0.0133 0.6369 5 A 0.8471 0.0062 0.1467 6 A 0.9191 0.0040 0.0769 7 L 0.9227 0.0037 0.0736 8 I 0.8627 0.0093 0.1281 9 F 0.5553 0.0137 0.4310 10 G 0.1538 0.0305 0.8157 11 G 0.0958 0.0391 0.8651 12 E 0.3019 0.0339 0.6642 13 T 0.5627 0.0231 0.4142 14 V 0.7447 0.0132 0.2421 15 V 0.8739 0.0062 0.1199 16 H 0.8859 0.0046 0.1095 17 V 0.7946 0.0084 0.1970 18 K 0.5522 0.0296 0.4182 19 G 0.2487 0.0466 0.7047 20 N 0.1289 0.0400 0.8311 21 G 0.1225 0.0375 0.8400 22 I 0.0838 0.0633 0.8528 23 G 0.0629 0.0688 0.8682 24 G 0.0628 0.1504 0.7868 25 R 0.0566 0.4494 0.4940 26 N 0.0408 0.7153 0.2439 27 Q 0.0108 0.9165 0.0727 28 E 0.0093 0.9401 0.0506 29 L 0.0082 0.9474 0.0444 30 A 0.0051 0.9563 0.0386 31 L 0.0051 0.9560 0.0390 32 S 0.0044 0.9550 0.0405 33 A 0.0045 0.9514 0.0441 34 A 0.0045 0.9505 0.0450 35 I 0.0048 0.9381 0.0571 36 A 0.0059 0.8992 0.0949 37 L 0.0116 0.8308 0.1576 38 E 0.0122 0.5511 0.4367 39 G 0.0281 0.2027 0.7692 40 I 0.0668 0.0761 0.8570 41 E 0.0357 0.1103 0.8540 42 G 0.0582 0.0601 0.8817 43 V 0.5368 0.0157 0.4475 44 I 0.8339 0.0152 0.1509 45 L 0.9123 0.0068 0.0809 46 C 0.9045 0.0084 0.0872 47 S 0.8506 0.0108 0.1386 48 A 0.6466 0.0350 0.3184 49 G 0.3380 0.0455 0.6165 50 T 0.1928 0.0643 0.7429 51 D 0.1561 0.0621 0.7817 52 G 0.1298 0.0487 0.8215 53 T 0.1688 0.0435 0.7878 54 D 0.1615 0.0390 0.7995 55 G 0.0890 0.0644 0.8467 56 P 0.0923 0.1655 0.7422 57 T 0.1108 0.2266 0.6627 58 D 0.1101 0.3291 0.5608 59 A 0.2058 0.2713 0.5229 60 A 0.2109 0.1483 0.6408 61 G 0.2893 0.0699 0.6408 62 G 0.5652 0.0419 0.3929 63 I 0.7266 0.0257 0.2477 64 V 0.5376 0.0251 0.4372 65 D 0.1950 0.0230 0.7821 66 G 0.0170 0.4803 0.5027 67 S 0.0139 0.6288 0.3573 68 T 0.0139 0.8033 0.1828 69 A 0.0051 0.9369 0.0580 70 K 0.0045 0.9445 0.0510 71 T 0.0044 0.9472 0.0484 72 L 0.0045 0.9419 0.0536 73 K 0.0050 0.9258 0.0693 74 A 0.0054 0.8159 0.1787 75 M 0.0391 0.3470 0.6139 76 G 0.0410 0.0564 0.9026 77 E 0.0612 0.0407 0.8981 78 D 0.1028 0.0343 0.8630 79 P 0.0069 0.8918 0.1013 80 Y 0.0061 0.9319 0.0620 81 Q 0.0055 0.9374 0.0571 82 Y 0.0053 0.9298 0.0649 83 L 0.0104 0.8734 0.1162 84 K 0.0099 0.7242 0.2659 85 N 0.0202 0.5657 0.4141 86 N 0.0591 0.3007 0.6402 87 D 0.0917 0.2198 0.6885 88 S 0.0253 0.7369 0.2378 89 Y 0.0061 0.9234 0.0704 90 N 0.0058 0.9393 0.0549 91 A 0.0051 0.9436 0.0513 92 L 0.0053 0.9416 0.0531 93 K 0.0063 0.9186 0.0751 94 K 0.0089 0.8118 0.1793 95 S 0.0486 0.5859 0.3655 96 G 0.0266 0.3777 0.5956 97 A 0.0698 0.3132 0.6170 98 L 0.3319 0.2995 0.3686 99 L 0.5898 0.1248 0.2854 100 I 0.5907 0.0689 0.3405 101 T 0.4551 0.0617 0.4832 102 G 0.1348 0.0363 0.8289 103 P 0.0786 0.0759 0.8455 104 T 0.0927 0.0697 0.8376 105 G 0.0913 0.0807 0.8279 106 T 0.1540 0.0751 0.7709 107 N 0.2711 0.0968 0.6321 108 V 0.2374 0.2226 0.5400 109 N 0.2562 0.1958 0.5480 110 D 0.5209 0.1505 0.3286 111 L 0.7099 0.0987 0.1914 112 I 0.7782 0.1010 0.1207 113 I 0.8322 0.0635 0.1044 114 G 0.8460 0.0462 0.1078 115 L 0.8120 0.0486 0.1394 116 I 0.6673 0.0322 0.3006 117 V 0.0814 0.0275 0.8911