# 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 30 # # ============================================ # 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 30 # # ============================================ # 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 30 # # ============================================ # 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 30 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0633 0.0236 0.9130 2 P 0.1145 0.0324 0.8531 3 A 0.2552 0.0452 0.6997 4 W 0.1860 0.0384 0.7756 5 P 0.1210 0.0312 0.8478 6 D 0.0979 0.0404 0.8617 7 S 0.0173 0.2935 0.6891 8 S 0.0270 0.2688 0.7042 9 T 0.0575 0.2471 0.6954 10 S 0.0084 0.7782 0.2134 11 E 0.0068 0.8270 0.1662 12 D 0.0079 0.8725 0.1196 13 A 0.0044 0.9526 0.0430 14 L 0.0044 0.9589 0.0367 15 K 0.0044 0.9587 0.0370 16 V 0.0044 0.9594 0.0363 17 L 0.0045 0.9557 0.0398 18 E 0.0048 0.9428 0.0524 19 K 0.0067 0.8731 0.1203 20 Y 0.0442 0.5242 0.4316 21 G 0.0373 0.0836 0.8791 22 I 0.0652 0.0675 0.8673 23 E 0.1071 0.0782 0.8147 24 T 0.0956 0.0309 0.8735 25 S 0.0796 0.0519 0.8685 26 E 0.0155 0.7312 0.2533 27 S 0.0202 0.7785 0.2013 28 V 0.0289 0.8170 0.1541 29 K 0.0438 0.7908 0.1654 30 R 0.0736 0.7280 0.1984 31 A 0.0895 0.6576 0.2529 32 I 0.1037 0.5296 0.3667 33 L 0.1081 0.3275 0.5644 34 Q 0.1046 0.1456 0.7497 35 E 0.0832 0.0953 0.8215 36 T 0.0743 0.0727 0.8530 37 P 0.0791 0.1375 0.7833 38 K 0.0567 0.2883 0.6551 39 H 0.0990 0.2635 0.6375 40 L 0.1822 0.1993 0.6186 41 S 0.1465 0.1887 0.6649 42 N 0.2141 0.1112 0.6747 43 V 0.4980 0.0281 0.4739 44 E 0.6519 0.0147 0.3334 45 I 0.8644 0.0063 0.1292 46 H 0.9069 0.0054 0.0877 47 L 0.9158 0.0045 0.0797 48 I 0.8816 0.0062 0.1123 49 G 0.6071 0.0234 0.3695 50 N 0.1920 0.0357 0.7724 51 V 0.0415 0.4132 0.5453 52 Q 0.0108 0.8263 0.1628 53 K 0.0081 0.9107 0.0812 54 V 0.0058 0.9338 0.0604 55 C 0.0046 0.9514 0.0440 56 D 0.0046 0.9557 0.0397 57 E 0.0044 0.9581 0.0375 58 A 0.0044 0.9571 0.0384 59 K 0.0044 0.9576 0.0380 60 S 0.0045 0.9549 0.0406 61 L 0.0045 0.9544 0.0410 62 A 0.0049 0.9515 0.0436 63 K 0.0049 0.9372 0.0579 64 E 0.0069 0.8776 0.1155 65 K 0.0421 0.3913 0.5666 66 G 0.0346 0.0268 0.9386 67 F 0.0810 0.0154 0.9036 68 N 0.2907 0.0167 0.6926 69 A 0.8478 0.0099 0.1423 70 E 0.9122 0.0074 0.0803 71 I 0.9197 0.0061 0.0742 72 I 0.8467 0.0232 0.1301 73 T 0.4811 0.0650 0.4540 74 T 0.1246 0.2387 0.6367 75 S 0.1195 0.3116 0.5689 76 L 0.1238 0.3712 0.5050 77 D 0.0945 0.4639 0.4416 78 C 0.0868 0.5274 0.3859 79 E 0.0834 0.7077 0.2090 80 A 0.0134 0.9062 0.0805 81 R 0.0071 0.9167 0.0761 82 E 0.0063 0.9255 0.0682 83 A 0.0046 0.9285 0.0669 84 G 0.0045 0.9479 0.0477 85 R 0.0045 0.9551 0.0404 86 F 0.0045 0.9544 0.0411 87 I 0.0044 0.9563 0.0392 88 A 0.0044 0.9570 0.0385 89 S 0.0044 0.9575 0.0381 90 I 0.0044 0.9572 0.0384 91 M 0.0044 0.9548 0.0408 92 K 0.0044 0.9537 0.0418 93 E 0.0045 0.9493 0.0462 94 V 0.0048 0.9414 0.0538 95 K 0.0057 0.9105 0.0839 96 F 0.0073 0.8162 0.1764 97 K 0.0443 0.3989 0.5568 98 D 0.0424 0.0397 0.9180 99 R 0.0806 0.0206 0.8988 100 P 0.1338 0.0280 0.8382 101 L 0.1212 0.0426 0.8362 102 K 0.0724 0.0330 0.8946 103 K 0.0929 0.0225 0.8846 104 P 0.3119 0.0093 0.6788 105 A 0.8541 0.0048 0.1411 106 A 0.9170 0.0038 0.0792 107 L 0.9253 0.0037 0.0710 108 I 0.8729 0.0085 0.1186 109 F 0.6503 0.0131 0.3366 110 G 0.2046 0.0300 0.7654 111 G 0.1164 0.0384 0.8452 112 E 0.3209 0.0321 0.6470 113 T 0.5669 0.0237 0.4093 114 V 0.7476 0.0131 0.2394 115 V 0.8737 0.0062 0.1202 116 H 0.8860 0.0046 0.1095 117 V 0.7938 0.0090 0.1971 118 K 0.5609 0.0293 0.4098 119 G 0.2600 0.0472 0.6928 120 N 0.1318 0.0400 0.8282 121 G 0.1242 0.0373 0.8385 122 I 0.0854 0.0634 0.8512 123 G 0.0638 0.0686 0.8676 124 G 0.0651 0.1471 0.7879 125 R 0.0580 0.4399 0.5022 126 N 0.0432 0.7089 0.2479 127 Q 0.0109 0.9170 0.0721 128 E 0.0091 0.9409 0.0500 129 L 0.0079 0.9481 0.0440 130 A 0.0047 0.9570 0.0383 131 L 0.0051 0.9564 0.0386 132 S 0.0044 0.9547 0.0408 133 A 0.0045 0.9518 0.0437 134 A 0.0045 0.9508 0.0447 135 I 0.0048 0.9395 0.0557 136 A 0.0057 0.9039 0.0904 137 L 0.0108 0.8365 0.1527 138 E 0.0118 0.5539 0.4343 139 G 0.0276 0.1999 0.7726 140 I 0.0701 0.0736 0.8563 141 E 0.0367 0.1037 0.8596 142 G 0.0551 0.0635 0.8814 143 V 0.4911 0.0242 0.4847 144 I 0.8033 0.0193 0.1773 145 L 0.8879 0.0127 0.0994 146 C 0.8440 0.0207 0.1353 147 S 0.6866 0.0294 0.2840 148 A 0.3355 0.0492 0.6154 149 G 0.1303 0.0348 0.8349 150 T 0.0546 0.0235 0.9220