# This file is the result of combining several RDB files, specifically # YGR034W.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR034W.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR034W.t2k.str2.rdb (weight 1.54758) # YGR034W.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 YGR034W.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR034W # 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 YGR034W.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 131 # # ============================================ # Comments from YGR034W.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR034W # 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 YGR034W.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 131 # # ============================================ # Comments from YGR034W.t2k.str2.rdb # ============================================ # TARGET YGR034W # 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 YGR034W.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 131 # # ============================================ # Comments from YGR034W.t2k.alpha.rdb # ============================================ # TARGET YGR034W # 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 YGR034W.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 131 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1572 0.0250 0.8179 2 L 0.3693 0.0278 0.6029 3 N 0.4381 0.0324 0.5295 4 Y 0.4209 0.0609 0.5183 5 C 0.4265 0.0547 0.5188 6 K 0.3828 0.0516 0.5656 7 T 0.1363 0.0317 0.8320 8 M 0.0576 0.1414 0.8010 9 Y 0.1173 0.1326 0.7501 10 V 0.2332 0.1003 0.6665 11 S 0.1971 0.0937 0.7092 12 S 0.0899 0.1611 0.7489 13 D 0.0880 0.1454 0.7666 14 R 0.0275 0.5766 0.3959 15 R 0.0225 0.7293 0.2482 16 K 0.0209 0.7808 0.1982 17 A 0.0328 0.7363 0.2309 18 R 0.0497 0.7331 0.2171 19 K 0.0565 0.7328 0.2107 20 A 0.0613 0.7029 0.2358 21 Y 0.0730 0.6524 0.2746 22 F 0.0870 0.4874 0.4256 23 T 0.0999 0.2211 0.6790 24 A 0.0755 0.0827 0.8419 25 P 0.0599 0.1272 0.8128 26 S 0.0420 0.2946 0.6634 27 S 0.0531 0.3497 0.5972 28 E 0.1200 0.3648 0.5152 29 R 0.2023 0.3595 0.4382 30 R 0.2622 0.3463 0.3915 31 V 0.3202 0.3351 0.3447 32 L 0.4157 0.2780 0.3062 33 L 0.4269 0.2204 0.3527 34 S 0.3056 0.1684 0.5259 35 A 0.2062 0.1368 0.6570 36 P 0.1292 0.1676 0.7032 37 L 0.0848 0.2264 0.6889 38 S 0.0576 0.1813 0.7611 39 K 0.0056 0.9180 0.0763 40 E 0.0048 0.9371 0.0581 41 L 0.0048 0.9414 0.0538 42 R 0.0055 0.9331 0.0615 43 A 0.0068 0.8950 0.0981 44 Q 0.0143 0.7646 0.2211 45 Y 0.0546 0.2653 0.6801 46 G 0.0586 0.0730 0.8684 47 I 0.1798 0.0652 0.7550 48 K 0.2779 0.0529 0.6692 49 A 0.4484 0.0380 0.5136 50 L 0.4375 0.0166 0.5459 51 P 0.5429 0.0121 0.4450 52 I 0.6185 0.0137 0.3678 53 R 0.4479 0.0179 0.5342 54 R 0.2249 0.0717 0.7034 55 D 0.0473 0.0434 0.9093 56 D 0.2401 0.0146 0.7453 57 E 0.8059 0.0037 0.1904 58 V 0.9178 0.0033 0.0789 59 L 0.9266 0.0035 0.0699 60 V 0.9248 0.0032 0.0720 61 V 0.8860 0.0125 0.1016 62 R 0.7718 0.0165 0.2117 63 G 0.3762 0.0394 0.5843 64 S 0.1680 0.0844 0.7476 65 K 0.1822 0.1030 0.7148 66 K 0.1218 0.0968 0.7814 67 G 0.0842 0.0618 0.8540 68 Q 0.3271 0.0562 0.6167 69 E 0.5398 0.0299 0.4304 70 G 0.5463 0.0156 0.4381 71 K 0.7278 0.0068 0.2654 72 I 0.8925 0.0032 0.1042 73 S 0.8594 0.0194 0.1212 74 S 0.9128 0.0042 0.0830 75 V 0.8922 0.0054 0.1024 76 Y 0.7817 0.0073 0.2110 77 R 0.3350 0.1418 0.5231 78 L 0.1304 0.2046 0.6649 79 K 0.1782 0.1290 0.6928 80 F 0.3101 0.0398 0.6501 81 A 0.8553 0.0049 0.1398 82 V 0.9223 0.0033 0.0744 83 Q 0.9228 0.0035 0.0736 84 V 0.8963 0.0052 0.0985 85 D 0.7822 0.0257 0.1921 86 K 0.6357 0.0188 0.3455 87 V 0.7408 0.0116 0.2477 88 T 0.8464 0.0093 0.1443 89 K 0.8698 0.0092 0.1210 90 E 0.8516 0.0106 0.1378 91 K 0.7790 0.0152 0.2059 92 V 0.4428 0.0397 0.5175 93 N 0.1612 0.0318 0.8070 94 G 0.3007 0.0394 0.6599 95 A 0.7686 0.0079 0.2235 96 S 0.8315 0.0060 0.1625 97 V 0.8047 0.0072 0.1881 98 P 0.7390 0.0126 0.2483 99 I 0.5832 0.0183 0.3985 100 N 0.5170 0.0187 0.4643 101 L 0.4971 0.0176 0.4853 102 H 0.3655 0.0192 0.6153 103 P 0.1980 0.1717 0.6303 104 S 0.1470 0.2118 0.6412 105 K 0.2337 0.1629 0.6034 106 L 0.6272 0.0243 0.3485 107 V 0.8627 0.0083 0.1290 108 I 0.9044 0.0065 0.0891 109 T 0.8026 0.0265 0.1708 110 K 0.6243 0.0204 0.3552 111 L 0.1921 0.2598 0.5481 112 H 0.1130 0.2147 0.6723 113 L 0.1103 0.1682 0.7215 114 D 0.0701 0.0668 0.8631 115 K 0.1297 0.0510 0.8193 116 D 0.2141 0.0675 0.7184 117 R 0.4089 0.0473 0.5438 118 K 0.7028 0.0211 0.2761 119 A 0.8038 0.0196 0.1767 120 L 0.8335 0.0209 0.1456 121 I 0.8540 0.0169 0.1291 122 Q 0.8309 0.0158 0.1533 123 R 0.7373 0.0306 0.2321 124 K 0.4396 0.0862 0.4742 125 G 0.0830 0.0665 0.8505 126 G 0.0541 0.0630 0.8830 127 K 0.2129 0.0657 0.7214 128 L 0.2444 0.0414 0.7142 129 E 0.0503 0.0280 0.9218