# This file is the result of combining several RDB files, specifically # T0545.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0545.t2k.stride-ebghtl.rdb (weight 1.24869) # T0545.t2k.str2.rdb (weight 1.54758) # T0545.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 T0545.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0545 # 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 T0545.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 382 # # ============================================ # Comments from T0545.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0545 # 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 T0545.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 382 # # ============================================ # Comments from T0545.t2k.str2.rdb # ============================================ # TARGET T0545 # 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 T0545.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 382 # # ============================================ # Comments from T0545.t2k.alpha.rdb # ============================================ # TARGET T0545 # 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 T0545.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 382 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1037 0.0337 0.8626 2 I 0.2630 0.0276 0.7094 3 K 0.3440 0.0401 0.6160 4 R 0.2999 0.0350 0.6652 5 G 0.2131 0.0358 0.7511 6 F 0.1853 0.0325 0.7821 7 P 0.1539 0.0398 0.8063 8 A 0.1607 0.0591 0.7802 9 V 0.2776 0.0987 0.6237 10 L 0.2988 0.0397 0.6615 11 D 0.0961 0.0382 0.8657 12 E 0.0195 0.1193 0.8611 13 N 0.0304 0.0536 0.9160 14 T 0.1768 0.0127 0.8105 15 E 0.5386 0.0180 0.4434 16 I 0.9302 0.0031 0.0667 17 L 0.9302 0.0035 0.0664 18 I 0.9273 0.0033 0.0694 19 L 0.8610 0.0139 0.1251 20 G 0.5366 0.0197 0.4438 21 S 0.2040 0.0302 0.7658 22 L 0.1122 0.0310 0.8568 23 P 0.0705 0.0856 0.8439 24 S 0.0552 0.1156 0.8292 25 D 0.0153 0.8176 0.1671 26 E 0.0114 0.8325 0.1561 27 S 0.0187 0.8406 0.1407 28 I 0.0115 0.8557 0.1328 29 R 0.0152 0.8136 0.1712 30 K 0.0400 0.5251 0.4349 31 Q 0.0441 0.2239 0.7319 32 Q 0.1550 0.1857 0.6592 33 Y 0.3233 0.1540 0.5228 34 Y 0.2059 0.1320 0.6621 35 G 0.1275 0.1015 0.7709 36 N 0.0793 0.0587 0.8620 37 P 0.0266 0.1843 0.7891 38 G 0.0368 0.1664 0.7968 39 N 0.0595 0.3167 0.6239 40 D 0.0475 0.6076 0.3449 41 F 0.0083 0.8732 0.1184 42 W 0.0055 0.9377 0.0569 43 R 0.0048 0.9549 0.0404 44 L 0.0047 0.9568 0.0385 45 V 0.0048 0.9535 0.0418 46 G 0.0049 0.9342 0.0609 47 H 0.0060 0.8916 0.1023 48 A 0.0186 0.7403 0.2411 49 I 0.0493 0.3889 0.5618 50 G 0.0498 0.1389 0.8113 51 E 0.0662 0.0924 0.8415 52 N 0.0637 0.1245 0.8118 53 L 0.0465 0.3461 0.6074 54 Q 0.0436 0.3731 0.5833 55 D 0.0419 0.3376 0.6205 56 M 0.0564 0.1827 0.7609 57 A 0.0609 0.1352 0.8039 58 Y 0.0213 0.7459 0.2328 59 E 0.0068 0.9015 0.0916 60 K 0.0063 0.9168 0.0769 61 K 0.0052 0.9393 0.0555 62 L 0.0056 0.9451 0.0493 63 K 0.0057 0.9415 0.0528 64 T 0.0054 0.9386 0.0561 65 L 0.0060 0.9363 0.0577 66 K 0.0055 0.9231 0.0713 67 H 0.0066 0.8692 0.1242 68 N 0.0443 0.5721 0.3835 69 R 0.0399 0.1038 0.8564 70 I 0.2238 0.0782 0.6980 71 G 0.5666 0.1011 0.3323 72 L 0.6553 0.1613 0.1834 73 W 0.4900 0.3219 0.1881 74 D 0.3386 0.4079 0.2535 75 V 0.1700 0.6322 0.1977 76 F 0.1406 0.6832 0.1762 77 K 0.1057 0.6646 0.2297 78 A 0.1022 0.5913 0.3064 79 G 0.1343 0.4889 0.3768 80 S 0.1190 0.4276 0.4534 81 R 0.0743 0.4095 0.5162 82 E 0.0421 0.2822 0.6757 83 G 0.0479 0.1685 0.7836 84 S 0.0672 0.2283 0.7045 85 Q 0.0503 0.3368 0.6129 86 D 0.0486 0.4119 0.5394 87 S 0.0484 0.4276 0.5240 88 K 0.0774 0.3881 0.5344 89 I 0.1349 0.3875 0.4776 90 G 0.1582 0.3809 0.4610 91 D 0.2023 0.2885 0.5092 92 E 0.1666 0.2249 0.6085 93 E 0.1554 0.1530 0.6916 94 I 0.1068 0.3267 0.5665 95 N 0.0806 0.3181 0.6012 96 D 0.0568 0.4507 0.4925 97 F 0.0137 0.8554 0.1308 98 S 0.0100 0.8940 0.0960 99 G 0.0091 0.9113 0.0796 100 L 0.0078 0.9177 0.0745 101 K 0.0081 0.9044 0.0875 102 E 0.0099 0.8361 0.1541 103 M 0.0175 0.6903 0.2922 104 V 0.0608 0.2649 0.6743 105 P 0.0582 0.1126 0.8292 106 K 0.1119 0.0726 0.8155 107 L 0.2425 0.1504 0.6071 108 R 0.4727 0.1337 0.3936 109 L 0.8019 0.0902 0.1078 110 I 0.8497 0.0692 0.0811 111 C 0.8207 0.0807 0.0985 112 F 0.6919 0.1361 0.1720 113 N 0.2790 0.1355 0.5855 114 G 0.0518 0.3888 0.5595 115 R 0.0201 0.8580 0.1219 116 K 0.0104 0.9210 0.0686 117 A 0.0059 0.9452 0.0489 118 G 0.0082 0.9475 0.0443 119 E 0.0116 0.9391 0.0493 120 Y 0.0090 0.9312 0.0598 121 E 0.0086 0.9137 0.0777 122 P 0.0104 0.8701 0.1195 123 L 0.0155 0.7968 0.1878 124 L 0.0354 0.6726 0.2921 125 R 0.0659 0.3420 0.5921 126 G 0.0541 0.2144 0.7314 127 M 0.0613 0.1959 0.7428 128 G 0.0775 0.1308 0.7917 129 Y 0.1776 0.0776 0.7448 130 E 0.3007 0.0566 0.6427 131 T 0.4784 0.0500 0.4716 132 K 0.5317 0.0277 0.4406 133 V 0.5239 0.0201 0.4560 134 L 0.3309 0.0198 0.6493 135 P 0.1665 0.0350 0.7985 136 S 0.1076 0.0493 0.8431 137 S 0.0814 0.0560 0.8625 138 S 0.0694 0.0495 0.8812 139 G 0.0435 0.4284 0.5281 140 A 0.0391 0.6021 0.3588 141 N 0.0567 0.6448 0.2985 142 R 0.0825 0.6357 0.2818 143 R 0.1165 0.5240 0.3594 144 F 0.1323 0.3599 0.5078 145 S 0.0990 0.2226 0.6785 146 K 0.0318 0.5924 0.3757 147 N 0.0060 0.8603 0.1337 148 R 0.0070 0.8568 0.1361 149 E 0.0074 0.8709 0.1216 150 S 0.0116 0.8758 0.1125 151 E 0.0150 0.8686 0.1164 152 W 0.0156 0.8704 0.1141 153 E 0.0308 0.8181 0.1511 154 A 0.0382 0.7587 0.2030 155 V 0.0481 0.6951 0.2568 156 F 0.0764 0.4543 0.4693 157 R 0.0704 0.2105 0.7191 158 H 0.0491 0.0374 0.9135