# This file is the result of combining several RDB files, specifically # T0459.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0459.t2k.stride-ebghtl.rdb (weight 1.24869) # T0459.t2k.str2.rdb (weight 1.54758) # T0459.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 T0459.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0459 # 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 T0459.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 875 # # ============================================ # Comments from T0459.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0459 # 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 T0459.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 875 # # ============================================ # Comments from T0459.t2k.str2.rdb # ============================================ # TARGET T0459 # 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 T0459.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 875 # # ============================================ # Comments from T0459.t2k.alpha.rdb # ============================================ # TARGET T0459 # 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 T0459.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 875 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1722 0.1593 0.6686 2 N 0.2280 0.2420 0.5300 3 A 0.2492 0.2664 0.4844 4 M 0.2873 0.2487 0.4641 5 L 0.3432 0.1629 0.4938 6 R 0.3257 0.0896 0.5847 7 Y 0.2005 0.1224 0.6771 8 G 0.0906 0.1082 0.8012 9 D 0.0878 0.0949 0.8172 10 T 0.0541 0.2374 0.7085 11 E 0.0474 0.3071 0.6455 12 I 0.0491 0.3189 0.6320 13 C 0.0468 0.2423 0.7109 14 I 0.0530 0.2229 0.7241 15 D 0.0595 0.2418 0.6987 16 P 0.0300 0.6720 0.2980 17 S 0.0052 0.9319 0.0629 18 E 0.0047 0.9524 0.0428 19 S 0.0047 0.9568 0.0385 20 V 0.0047 0.9573 0.0380 21 L 0.0051 0.9550 0.0399 22 H 0.0052 0.9437 0.0510 23 L 0.0060 0.9183 0.0757 24 L 0.0230 0.7995 0.1776 25 G 0.0249 0.5078 0.4673 26 K 0.0150 0.3629 0.6221 27 K 0.0371 0.5980 0.3649 28 Y 0.0897 0.6860 0.2243 29 T 0.0490 0.8619 0.0891 30 M 0.0350 0.9158 0.0492 31 L 0.0184 0.9398 0.0419 32 I 0.0227 0.9367 0.0406 33 I 0.0172 0.9380 0.0448 34 S 0.0155 0.9292 0.0553 35 V 0.0087 0.9239 0.0674 36 L 0.0143 0.8521 0.1336 37 G 0.0199 0.6235 0.3566 38 N 0.0234 0.3497 0.6269 39 G 0.0285 0.2231 0.7484 40 S 0.0489 0.1411 0.8100 41 T 0.0547 0.0864 0.8589 42 R 0.1287 0.1608 0.7104 43 Q 0.2420 0.2068 0.5512 44 N 0.1893 0.2078 0.6029 45 F 0.0277 0.7832 0.1891 46 N 0.0114 0.8778 0.1107 47 D 0.0065 0.9220 0.0716 48 I 0.0067 0.9250 0.0684 49 R 0.0070 0.8839 0.1091 50 S 0.0073 0.7580 0.2347 51 S 0.0164 0.6685 0.3150 52 I 0.0556 0.2799 0.6645 53 P 0.0166 0.2308 0.7526 54 G 0.0235 0.1682 0.8083 55 I 0.0895 0.1828 0.7277 56 S 0.0699 0.1723 0.7578 57 S 0.0052 0.8919 0.1029 58 T 0.0049 0.9186 0.0765 59 I 0.0053 0.9336 0.0611 60 L 0.0048 0.9413 0.0539 61 S 0.0050 0.9482 0.0468 62 R 0.0050 0.9488 0.0462 63 R 0.0051 0.9534 0.0415 64 I 0.0048 0.9550 0.0403 65 K 0.0050 0.9565 0.0385 66 D 0.0050 0.9552 0.0398 67 L 0.0056 0.9523 0.0421 68 I 0.0068 0.9389 0.0543 69 D 0.0082 0.8726 0.1191 70 S 0.0449 0.2950 0.6602 71 G 0.0356 0.0424 0.9220 72 L 0.1531 0.0568 0.7901 73 V 0.6389 0.0394 0.3217 74 E 0.6767 0.0337 0.2897 75 R 0.5350 0.0227 0.4423 76 R 0.3229 0.0148 0.6623 77 S 0.1294 0.0214 0.8492 78 G 0.0853 0.0116 0.9031 79 Q 0.1313 0.0253 0.8434 80 I 0.6109 0.0087 0.3804 81 T 0.8365 0.0058 0.1577 82 T 0.8915 0.0069 0.1016 83 Y 0.8853 0.0060 0.1087 84 A 0.8506 0.0055 0.1439 85 L 0.6365 0.0118 0.3517 86 T 0.1719 0.0202 0.8079 87 E 0.0231 0.3146 0.6623 88 K 0.0252 0.3566 0.6182 89 G 0.0231 0.5334 0.4435 90 M 0.0252 0.6486 0.3262 91 N 0.0574 0.6483 0.2942 92 V 0.0155 0.8557 0.1287 93 R 0.0081 0.9193 0.0726 94 N 0.0051 0.9392 0.0558 95 S 0.0049 0.9476 0.0475 96 L 0.0048 0.9531 0.0421 97 M 0.0047 0.9546 0.0407 98 P 0.0047 0.9563 0.0390 99 L 0.0048 0.9544 0.0409 100 L 0.0048 0.9552 0.0400 101 Q 0.0048 0.9489 0.0463 102 Y 0.0056 0.9347 0.0597 103 I 0.0069 0.9078 0.0854 104 S 0.0063 0.8840 0.1097 105 V 0.0107 0.7946 0.1947 106 L 0.0239 0.6020 0.3741 107 D 0.0388 0.2697 0.6915 108 R 0.0410 0.1985 0.7605 109 N 0.0489 0.1653 0.7858 110 G 0.0441 0.1234 0.8325 111 D 0.0650 0.0357 0.8993