# This file is the result of combining several RDB files, specifically # T0196.t04.dssp-ebghstl.rdb (weight 1.53986) # T0196.t04.stride-ebghtl.rdb (weight 1.24869) # T0196.t04.str2.rdb (weight 1.54758) # T0196.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 T0196.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0196 # 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 T0196.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 2.67669 # # ============================================ # Comments from T0196.t04.stride-ebghtl.rdb # ============================================ # TARGET T0196 # 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 T0196.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 2.67669 # # ============================================ # Comments from T0196.t04.str2.rdb # ============================================ # TARGET T0196 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0196.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 2.67669 # # ============================================ # Comments from T0196.t04.alpha.rdb # ============================================ # TARGET T0196 # 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 T0196.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 2.67669 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.1368 0.2759 0.5873 2 H 0.1623 0.2712 0.5665 3 H 0.1649 0.2537 0.5814 4 H 0.1511 0.2304 0.6185 5 H 0.1366 0.2038 0.6596 6 H 0.1183 0.1781 0.7035 7 H 0.0864 0.1542 0.7594 8 G 0.0627 0.1738 0.7635 9 S 0.0612 0.3448 0.5940 10 G 0.0922 0.4379 0.4699 11 L 0.0607 0.7469 0.1924 12 F 0.0622 0.7921 0.1457 13 D 0.0534 0.8223 0.1243 14 F 0.0568 0.8265 0.1166 15 L 0.0771 0.7592 0.1637 16 K 0.1069 0.6393 0.2537 17 R 0.1032 0.5849 0.3119 18 K 0.0787 0.4318 0.4894 19 E 0.0908 0.3101 0.5991 20 V 0.1004 0.3311 0.5685 21 K 0.0899 0.2863 0.6238 22 E 0.0595 0.7065 0.2340 23 E 0.0738 0.7270 0.1992 24 E 0.1307 0.6745 0.1948 25 K 0.1615 0.6910 0.1475 26 I 0.2098 0.6531 0.1372 27 E 0.2161 0.6405 0.1435 28 I 0.2272 0.6043 0.1685 29 L 0.1956 0.4512 0.3532 30 S 0.1266 0.1984 0.6750 31 K 0.1011 0.0871 0.8118 32 K 0.1113 0.0244 0.8643 33 P 0.1538 0.0461 0.8000 34 A 0.1742 0.0942 0.7316 35 G 0.2315 0.0606 0.7079 36 K 0.6465 0.0351 0.3183 37 V 0.8192 0.0093 0.1715 38 V 0.8619 0.0080 0.1302 39 V 0.8693 0.0262 0.1044 40 E 0.7861 0.0791 0.1348 41 E 0.7953 0.0545 0.1502 42 V 0.8112 0.0720 0.1167 43 V 0.8172 0.0797 0.1031 44 N 0.7985 0.0797 0.1217 45 I 0.6855 0.0962 0.2183 46 M 0.4199 0.0739 0.5062 47 G 0.2484 0.0609 0.6907 48 K 0.2838 0.0629 0.6533 49 D 0.4901 0.0375 0.4724 50 V 0.8368 0.0118 0.1514 51 I 0.9099 0.0088 0.0813 52 I 0.8880 0.0167 0.0952 53 G 0.8115 0.0225 0.1660 54 T 0.7755 0.0224 0.2021 55 V 0.6957 0.0630 0.2413 56 E 0.6053 0.0950 0.2997 57 S 0.3790 0.1353 0.4857 58 G 0.3414 0.0870 0.5716 59 M 0.6921 0.0417 0.2662 60 I 0.8045 0.0319 0.1635 61 G 0.7773 0.0268 0.1960 62 V 0.7453 0.0288 0.2259 63 G 0.7610 0.0238 0.2153 64 F 0.8483 0.0102 0.1415 65 K 0.8870 0.0077 0.1053 66 V 0.8275 0.0103 0.1621 67 K 0.5542 0.0375 0.4084 68 G 0.2014 0.0247 0.7739 69 P 0.0830 0.0728 0.8442 70 S 0.0668 0.0950 0.8382 71 G 0.1549 0.0787 0.7663 72 I 0.4103 0.0440 0.5456 73 G 0.6507 0.0380 0.3113 74 G 0.8113 0.0154 0.1733 75 I 0.8924 0.0136 0.0939 76 V 0.8930 0.0150 0.0920 77 R 0.8960 0.0121 0.0919 78 I 0.8330 0.0304 0.1366 79 E 0.6570 0.0608 0.2821 80 R 0.3879 0.1030 0.5091 81 N 0.1529 0.0851 0.7620 82 R 0.1512 0.0863 0.7625 83 E 0.3789 0.0559 0.5651 84 K 0.7545 0.0335 0.2121 85 V 0.8012 0.0208 0.1780 86 E 0.8544 0.0248 0.1208 87 F 0.8587 0.0232 0.1181 88 A 0.7958 0.0265 0.1777 89 I 0.6255 0.0314 0.3431 90 A 0.2704 0.0873 0.6423 91 G 0.0938 0.0643 0.8419 92 D 0.1885 0.0862 0.7253 93 R 0.4290 0.1219 0.4491 94 I 0.5967 0.0745 0.3288 95 G 0.7515 0.0454 0.2031 96 I 0.8329 0.0305 0.1366 97 S 0.8440 0.0318 0.1242 98 I 0.8051 0.0518 0.1430 99 E 0.6939 0.0799 0.2263 100 G 0.3644 0.1274 0.5082 101 K 0.3232 0.1262 0.5505 102 I 0.3008 0.1554 0.5438 103 G 0.1944 0.0852 0.7204 104 K 0.3264 0.0654 0.6082 105 V 0.3598 0.0406 0.5996 106 K 0.2404 0.0493 0.7103 107 K 0.1339 0.1542 0.7119 108 G 0.0913 0.0684 0.8403 109 D 0.3112 0.0371 0.6517 110 V 0.7686 0.0528 0.1785 111 L 0.8328 0.0478 0.1195 112 E 0.8693 0.0436 0.0870 113 I 0.8880 0.0206 0.0914 114 Y 0.7997 0.0248 0.1754 115 Q 0.6214 0.0188 0.3597 116 T 0.2094 0.0264 0.7642