# This file is the result of combining several RDB files, specifically # T0317.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0317.t2k.stride-ebghtl.rdb (weight 1.24869) # T0317.t2k.str2.rdb (weight 1.54758) # T0317.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 T0317.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0317 # 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 T0317.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 733 # # ============================================ # Comments from T0317.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0317 # 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 T0317.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 733 # # ============================================ # Comments from T0317.t2k.str2.rdb # ============================================ # TARGET T0317 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0317.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 733 # # ============================================ # Comments from T0317.t2k.alpha.rdb # ============================================ # TARGET T0317 # 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 T0317.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 733 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0673 0.0569 0.8758 2 G 0.1481 0.0705 0.7814 3 T 0.2097 0.0858 0.7045 4 S 0.1827 0.1223 0.6951 5 E 0.1231 0.1894 0.6875 6 A 0.0920 0.1669 0.7410 7 A 0.0788 0.1156 0.8055 8 P 0.0836 0.0812 0.8352 9 P 0.0890 0.0761 0.8349 10 P 0.1208 0.1140 0.7653 11 F 0.2044 0.2532 0.5424 12 A 0.3402 0.2255 0.4343 13 R 0.4916 0.1565 0.3519 14 V 0.4400 0.1076 0.4524 15 A 0.2155 0.0746 0.7099 16 P 0.0572 0.1765 0.7663 17 A 0.1340 0.1329 0.7332 18 L 0.6111 0.0452 0.3437 19 F 0.7958 0.0213 0.1829 20 I 0.7134 0.0434 0.2432 21 G 0.3650 0.0451 0.5899 22 N 0.1830 0.0594 0.7576 23 A 0.1092 0.2210 0.6697 24 R 0.0611 0.3788 0.5600 25 A 0.0453 0.4536 0.5011 26 A 0.0252 0.5559 0.4189 27 G 0.0311 0.4592 0.5097 28 A 0.0473 0.4150 0.5377 29 T 0.0091 0.8710 0.1199 30 E 0.0059 0.9384 0.0558 31 L 0.0049 0.9491 0.0460 32 L 0.0051 0.9527 0.0422 33 V 0.0051 0.9441 0.0508 34 R 0.0069 0.8767 0.1164 35 A 0.0449 0.3125 0.6426 36 G 0.0473 0.0176 0.9351 37 I 0.1213 0.0072 0.8715 38 T 0.5641 0.0199 0.4160 39 L 0.9249 0.0037 0.0714 40 C 0.9326 0.0032 0.0642 41 V 0.9263 0.0039 0.0698 42 N 0.8949 0.0041 0.1010 43 V 0.5625 0.0292 0.4083 44 S 0.2535 0.0504 0.6960 45 R 0.1377 0.1417 0.7206 46 Q 0.1341 0.1341 0.7317 47 Q 0.1340 0.1021 0.7639 48 P 0.1104 0.1298 0.7598 49 G 0.0933 0.1394 0.7673 50 P 0.0903 0.1667 0.7429 51 R 0.0953 0.1261 0.7786 52 A 0.0754 0.1375 0.7871 53 P 0.0656 0.1328 0.8015 54 G 0.1080 0.0981 0.7938 55 V 0.2793 0.0362 0.6845 56 A 0.5970 0.0247 0.3783 57 E 0.8008 0.0140 0.1852 58 L 0.7963 0.0177 0.1860 59 R 0.7907 0.0106 0.1987 60 V 0.6738 0.0095 0.3167 61 P 0.4472 0.0137 0.5391 62 V 0.1945 0.1057 0.6998 63 F 0.1380 0.1380 0.7240 64 D 0.0693 0.1267 0.8040 65 D 0.0530 0.0896 0.8574 66 P 0.0358 0.1455 0.8187 67 A 0.0743 0.1792 0.7465 68 E 0.0600 0.2260 0.7140 69 D 0.0905 0.2722 0.6373 70 L 0.0195 0.7910 0.1895 71 L 0.0073 0.8551 0.1376 72 T 0.0059 0.8453 0.1488 73 H 0.0086 0.8354 0.1560 74 L 0.0079 0.8568 0.1353 75 E 0.0048 0.9409 0.0542 76 P 0.0048 0.9455 0.0496 77 T 0.0048 0.9567 0.0386 78 C 0.0047 0.9596 0.0357 79 A 0.0047 0.9595 0.0358 80 A 0.0047 0.9581 0.0372 81 M 0.0047 0.9571 0.0382 82 E 0.0047 0.9556 0.0396 83 A 0.0048 0.9529 0.0423 84 A 0.0050 0.9490 0.0460 85 V 0.0066 0.9286 0.0648 86 R 0.0093 0.8550 0.1356 87 D 0.0404 0.3298 0.6298 88 G 0.0388 0.0261 0.9351 89 G 0.0903 0.0190 0.8907 90 S 0.4444 0.0064 0.5492 91 C 0.8981 0.0036 0.0983 92 L 0.9291 0.0032 0.0678 93 V 0.9257 0.0035 0.0707 94 Y 0.8890 0.0066 0.1044 95 C 0.5533 0.0372 0.4095 96 K 0.2301 0.1008 0.6692 97 N 0.0684 0.1070 0.8246 98 G 0.0565 0.0809 0.8626 99 R 0.0853 0.1711 0.7436 100 S 0.1150 0.2399 0.6451 101 R 0.0315 0.6352 0.3333 102 S 0.0090 0.8287 0.1623 103 A 0.0047 0.9547 0.0406 104 A 0.0047 0.9599 0.0355 105 V 0.0047 0.9605 0.0348 106 C 0.0047 0.9611 0.0343 107 T 0.0047 0.9607 0.0346 108 A 0.0047 0.9602 0.0351 109 Y 0.0047 0.9605 0.0348 110 L 0.0047 0.9597 0.0356 111 M 0.0051 0.9556 0.0392 112 R 0.0060 0.9394 0.0546 113 H 0.0110 0.8548 0.1342 114 R 0.0417 0.4404 0.5178 115 G 0.0378 0.0337 0.9285 116 H 0.0754 0.0212 0.9034 117 S 0.0958 0.0190 0.8851 118 L 0.0051 0.9423 0.0525 119 D 0.0047 0.9576 0.0377 120 R 0.0047 0.9590 0.0363 121 A 0.0047 0.9592 0.0361 122 F 0.0047 0.9588 0.0365 123 Q 0.0047 0.9576 0.0378 124 M 0.0047 0.9548 0.0404 125 V 0.0053 0.9469 0.0478 126 K 0.0056 0.9285 0.0659 127 S 0.0090 0.8212 0.1698 128 A 0.0227 0.6294 0.3479 129 R 0.0702 0.1375 0.7923 130 P 0.0407 0.1670 0.7923 131 V 0.0718 0.1597 0.7685 132 A 0.2238 0.0836 0.6926 133 E 0.1759 0.0421 0.7820 134 P 0.0913 0.0761 0.8326 135 N 0.0729 0.0890 0.8381 136 L 0.0065 0.7698 0.2236 137 G 0.0079 0.8400 0.1520 138 F 0.0048 0.9415 0.0537 139 W 0.0047 0.9564 0.0390 140 A 0.0047 0.9562 0.0392 141 Q 0.0047 0.9552 0.0401 142 L 0.0047 0.9571 0.0382 143 Q 0.0047 0.9566 0.0386 144 K 0.0048 0.9525 0.0427 145 Y 0.0048 0.9497 0.0455 146 E 0.0048 0.9494 0.0458 147 Q 0.0050 0.9441 0.0509 148 T 0.0056 0.9267 0.0677 149 L 0.0095 0.8886 0.1018 150 Q 0.0131 0.7985 0.1884 151 A 0.0205 0.5859 0.3936 152 Q 0.0349 0.3071 0.6580 153 A 0.0879 0.1645 0.7477 154 I 0.1665 0.1037 0.7298 155 L 0.1598 0.0842 0.7560 156 P 0.1471 0.0798 0.7731 157 R 0.1294 0.0939 0.7767 158 E 0.1145 0.0860 0.7994 159 P 0.1039 0.0933 0.8028 160 I 0.0941 0.0813 0.8246 161 D 0.0747 0.0725 0.8528 162 P 0.0428 0.1507 0.8066 163 E 0.0351 0.1954 0.7695