# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-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 18.617 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-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 18.617 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.t04-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 18.617 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t04-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 18.617 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0855 0.1464 0.7681 2 G 0.0688 0.0926 0.8385 3 H 0.0876 0.1093 0.8031 4 L 0.0941 0.0823 0.8236 5 E 0.0616 0.0725 0.8659 6 K 0.0269 0.5506 0.4225 7 P 0.0061 0.8604 0.1336 8 E 0.0067 0.9320 0.0613 9 V 0.0061 0.9499 0.0440 10 R 0.0047 0.9561 0.0393 11 R 0.0046 0.9612 0.0341 12 L 0.0046 0.9617 0.0336 13 A 0.0047 0.9612 0.0342 14 E 0.0048 0.9567 0.0385 15 E 0.0052 0.9449 0.0499 16 A 0.0426 0.5651 0.3923 17 G 0.0425 0.0285 0.9291 18 L 0.0707 0.0179 0.9114 19 S 0.1509 0.0783 0.7708 20 T 0.3229 0.1657 0.5114 21 A 0.3333 0.1565 0.5102 22 K 0.2726 0.1222 0.6052 23 K 0.1670 0.1087 0.7243 24 K 0.0909 0.2044 0.7047 25 D 0.0982 0.1910 0.7108 26 S 0.2560 0.1287 0.6153 27 T 0.2494 0.0856 0.6649 28 G 0.4221 0.0530 0.5249 29 I 0.8143 0.0109 0.1748 30 C 0.8886 0.0095 0.1019 31 F 0.8698 0.0088 0.1214 32 I 0.6322 0.0241 0.3437 33 G 0.2094 0.0292 0.7615 34 E 0.0804 0.1198 0.7998 35 K 0.0451 0.2028 0.7521 36 N 0.0723 0.2666 0.6611 37 F 0.0150 0.8562 0.1288 38 K 0.0062 0.9124 0.0813 39 N 0.0072 0.9038 0.0890 40 F 0.0188 0.8970 0.0842 41 L 0.0164 0.8842 0.0994 42 S 0.0082 0.8625 0.1293 43 N 0.0157 0.6721 0.3122 44 Y 0.0509 0.3982 0.5509 45 L 0.0798 0.0422 0.8780 46 P 0.0824 0.0531 0.8645 47 A 0.1397 0.0339 0.8264 48 Q 0.1245 0.0233 0.8522 49 P 0.1071 0.0621 0.8308 50 G 0.2276 0.0358 0.7366 51 R 0.6405 0.0150 0.3445 52 M 0.8898 0.0047 0.1055 53 M 0.8772 0.0056 0.1172 54 T 0.6713 0.0078 0.3209 55 V 0.2123 0.0767 0.7110 56 D 0.0448 0.0327 0.9226 57 G 0.0614 0.0343 0.9043 58 R 0.4510 0.0198 0.5292 59 D 0.8369 0.0129 0.1502 60 M 0.7590 0.0417 0.1993 61 G 0.6677 0.0415 0.2908 62 E 0.5971 0.0643 0.3386 63 H 0.4775 0.0739 0.4486 64 A 0.2237 0.0876 0.6887 65 G 0.3496 0.0442 0.6062 66 L 0.6582 0.0398 0.3020 67 M 0.8341 0.0206 0.1453 68 Y 0.8568 0.0237 0.1195 69 Y 0.8420 0.0329 0.1251 70 T 0.7512 0.0582 0.1905 71 I 0.5499 0.1756 0.2745 72 G 0.4598 0.1347 0.4055 73 Q 0.4548 0.1874 0.3578 74 R 0.3921 0.1901 0.4178 75 G 0.2218 0.1874 0.5908 76 G 0.1933 0.1272 0.6795 77 L 0.2570 0.1006 0.6424 78 G 0.3081 0.0755 0.6164 79 I 0.2756 0.1276 0.5968 80 G 0.2534 0.1115 0.6351 81 G 0.1846 0.1190 0.6964 82 Q 0.1514 0.1374 0.7112 83 H 0.1158 0.1265 0.7577 84 G 0.0690 0.0982 0.8327 85 G 0.0598 0.1174 0.8227 86 D 0.0856 0.0938 0.8206 87 N 0.1086 0.0547 0.8368 88 A 0.1787 0.0142 0.8071 89 P 0.3566 0.0138 0.6296 90 W 0.7206 0.0177 0.2617 91 F 0.8814 0.0091 0.1095 92 V 0.8984 0.0065 0.0951 93 V 0.8303 0.0284 0.1413 94 G 0.7581 0.0201 0.2217 95 K 0.6299 0.0295 0.3405 96 D 0.4543 0.0392 0.5065 97 L 0.1117 0.2874 0.6009 98 S 0.0803 0.2706 0.6491 99 K 0.1057 0.1985 0.6958 100 N 0.1992 0.0342 0.7666 101 I 0.7828 0.0069 0.2103 102 L 0.9198 0.0035 0.0767 103 Y 0.9234 0.0038 0.0728 104 V 0.8749 0.0114 0.1137 105 G 0.5690 0.0122 0.4188 106 Q 0.1946 0.0486 0.7568 107 G 0.0708 0.0577 0.8716 108 F 0.0881 0.0927 0.8192 109 Y 0.0935 0.1032 0.8033 110 H 0.0791 0.1584 0.7625 111 D 0.0306 0.4666 0.5027 112 S 0.0472 0.5926 0.3602 113 L 0.1447 0.4875 0.3678 114 M 0.2340 0.3281 0.4379 115 S 0.2633 0.2357 0.5010 116 T 0.2607 0.1735 0.5658 117 S 0.5396 0.0809 0.3795 118 L 0.7383 0.0238 0.2379 119 E 0.7751 0.0218 0.2031 120 A 0.6655 0.0700 0.2645 121 S 0.3851 0.1526 0.4624 122 Q 0.3750 0.1394 0.4856 123 V 0.5042 0.0838 0.4120 124 H 0.5616 0.0844 0.3540 125 F 0.5124 0.1093 0.3783 126 T 0.4014 0.1294 0.4693 127 R 0.2426 0.1253 0.6320 128 E 0.1499 0.0820 0.7682 129 M 0.1041 0.0236 0.8723 130 P 0.0637 0.0354 0.9009