# This file is the result of combining several RDB files, specifically # YGR230W.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR230W.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR230W.t2k.str2.rdb (weight 1.54758) # YGR230W.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 YGR230W.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR230W # 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 YGR230W.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 4 # # ============================================ # Comments from YGR230W.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR230W # 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 YGR230W.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 4 # # ============================================ # Comments from YGR230W.t2k.str2.rdb # ============================================ # TARGET YGR230W # 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 YGR230W.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 4 # # ============================================ # Comments from YGR230W.t2k.alpha.rdb # ============================================ # TARGET YGR230W # 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 YGR230W.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 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0822 0.0323 0.8855 2 S 0.1405 0.0530 0.8065 3 Y 0.0971 0.0989 0.8040 4 G 0.0681 0.0936 0.8383 5 G 0.0769 0.1054 0.8177 6 S 0.0913 0.2054 0.7033 7 A 0.0512 0.4628 0.4860 8 S 0.0364 0.5800 0.3836 9 Q 0.0152 0.8133 0.1715 10 D 0.0118 0.8857 0.1025 11 I 0.0091 0.9253 0.0657 12 V 0.0085 0.9387 0.0529 13 T 0.0095 0.9413 0.0492 14 K 0.0084 0.9453 0.0462 15 L 0.0073 0.9444 0.0483 16 I 0.0079 0.9361 0.0560 17 R 0.0104 0.9088 0.0808 18 K 0.0168 0.8386 0.1446 19 I 0.0454 0.6999 0.2546 20 Q 0.0582 0.4464 0.4954 21 N 0.0862 0.1772 0.7366 22 T 0.1352 0.0898 0.7750 23 S 0.2652 0.0443 0.6906 24 V 0.4297 0.0582 0.5121 25 S 0.4846 0.0623 0.4532 26 C 0.4344 0.0760 0.4897 27 T 0.3688 0.0879 0.5433 28 R 0.2742 0.1180 0.6079 29 R 0.1633 0.1815 0.6552 30 D 0.1268 0.1947 0.6785 31 E 0.0653 0.2691 0.6657 32 N 0.0878 0.2025 0.7098 33 L 0.0678 0.3392 0.5929 34 D 0.0510 0.4135 0.5355 35 S 0.0505 0.5172 0.4323 36 F 0.0504 0.6062 0.3434 37 N 0.0618 0.6012 0.3370 38 Q 0.0695 0.6284 0.3020 39 H 0.1161 0.5987 0.2852 40 L 0.2023 0.5506 0.2471 41 K 0.2777 0.4692 0.2531 42 M 0.3496 0.4217 0.2287 43 S 0.4249 0.3724 0.2026 44 L 0.4546 0.3479 0.1976 45 K 0.4556 0.3233 0.2211 46 V 0.3998 0.3516 0.2487 47 A 0.2671 0.3782 0.3547 48 H 0.1719 0.3137 0.5144 49 N 0.1154 0.2709 0.6137 50 T 0.0956 0.3248 0.5795 51 K 0.0682 0.5216 0.4103 52 T 0.0648 0.6035 0.3317 53 F 0.0451 0.7469 0.2081 54 A 0.0427 0.7548 0.2025 55 K 0.0385 0.7504 0.2111 56 H 0.0440 0.7531 0.2029 57 C 0.0441 0.7455 0.2104 58 L 0.0391 0.7646 0.1962 59 H 0.0305 0.8037 0.1657 60 R 0.0207 0.8598 0.1195 61 Q 0.0257 0.8637 0.1106 62 V 0.0264 0.8607 0.1129 63 F 0.0342 0.8267 0.1391 64 K 0.0283 0.8065 0.1652 65 N 0.0321 0.7134 0.2545 66 T 0.0499 0.5913 0.3588 67 Y 0.0758 0.5124 0.4118 68 R 0.1014 0.4724 0.4263 69 K 0.0724 0.5620 0.3656 70 R 0.0616 0.5893 0.3491 71 K 0.0703 0.5341 0.3956 72 A 0.0825 0.5047 0.4128 73 V 0.0918 0.4295 0.4787 74 E 0.0697 0.3956 0.5347 75 D 0.0782 0.2616 0.6602 76 Q 0.0217 0.5073 0.4710 77 R 0.0278 0.5133 0.4589 78 K 0.0347 0.5389 0.4264 79 N 0.0527 0.4927 0.4546 80 L 0.0538 0.5726 0.3736 81 N 0.0466 0.6018 0.3516 82 T 0.0465 0.6891 0.2644 83 Q 0.0507 0.7281 0.2212 84 L 0.0514 0.7582 0.1904 85 R 0.0689 0.6944 0.2367 86 Q 0.0846 0.6104 0.3050 87 K 0.1359 0.4742 0.3899 88 F 0.1728 0.2358 0.5913 89 A 0.1822 0.1031 0.7147 90 S 0.0951 0.0495 0.8555 91 P 0.0287 0.3015 0.6698 92 S 0.0374 0.2662 0.6964 93 D 0.0475 0.2900 0.6625 94 N 0.0799 0.2494 0.6708 95 L 0.1741 0.2250 0.6008 96 L 0.2029 0.2159 0.5811 97 S 0.1095 0.2311 0.6594 98 P 0.0492 0.5334 0.4175 99 C 0.0548 0.5435 0.4017 100 S 0.0360 0.6982 0.2658 101 R 0.0391 0.7478 0.2130 102 K 0.0534 0.6788 0.2678 103 L 0.0390 0.7384 0.2226 104 N 0.0230 0.7350 0.2420 105 D 0.0116 0.7783 0.2101 106 H 0.0315 0.6949 0.2736 107 K 0.0369 0.7119 0.2512 108 S 0.0549 0.7012 0.2439 109 K 0.0632 0.6970 0.2398 110 L 0.0802 0.6413 0.2785 111 F 0.0817 0.5510 0.3673 112 S 0.0703 0.4722 0.4575 113 A 0.0725 0.3880 0.5395 114 K 0.0743 0.2985 0.6271 115 S 0.0757 0.1629 0.7614 116 Q 0.0784 0.0882 0.8334 117 P 0.1018 0.1220 0.7763 118 K 0.1552 0.1915 0.6533 119 T 0.2337 0.2198 0.5466 120 L 0.1807 0.4792 0.3402 121 E 0.2063 0.5167 0.2771 122 F 0.2018 0.4890 0.3092 123 V 0.1937 0.3783 0.4280 124 R 0.1155 0.2619 0.6226 125 G 0.0766 0.1401 0.7833 126 K 0.1385 0.1291 0.7324 127 Q 0.2291 0.1184 0.6525 128 N 0.1652 0.0995 0.7353 129 I 0.1157 0.0490 0.8353 130 P 0.1012 0.0569 0.8420 131 R 0.1274 0.0860 0.7866 132 K 0.1106 0.0608 0.8286 133 P 0.1027 0.1052 0.7921 134 N 0.1077 0.0877 0.8046 135 V 0.1463 0.0626 0.7911 136 D 0.1189 0.0395 0.8416 137 I 0.0431 0.0425 0.9143