# This file is the result of combining several RDB files, specifically # T0285.t06.dssp-ebghstl.rdb (weight 1.53986) # T0285.t06.stride-ebghtl.rdb (weight 1.24869) # T0285.t06.str2.rdb (weight 1.54758) # T0285.t06.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 T0285.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0285 # Using neural net t06-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 T0285.t06-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 1 # # ============================================ # Comments from T0285.t06.stride-ebghtl.rdb # ============================================ # TARGET T0285 # Using neural net t06-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 T0285.t06-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 1 # # ============================================ # Comments from T0285.t06.str2.rdb # ============================================ # TARGET T0285 # Using neural net t06-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 T0285.t06-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 1 # # ============================================ # Comments from T0285.t06.alpha.rdb # ============================================ # TARGET T0285 # Using neural net t06-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 T0285.t06-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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.1006 0.1504 0.7490 2 Y 0.1667 0.1001 0.7332 3 L 0.1170 0.0244 0.8586 4 P 0.0622 0.0585 0.8793 5 D 0.0393 0.1098 0.8510 6 D 0.0411 0.0903 0.8686 7 S 0.0599 0.0696 0.8705 8 P 0.0242 0.6207 0.3551 9 A 0.0187 0.7876 0.1937 10 K 0.0252 0.8311 0.1437 11 R 0.0483 0.8423 0.1093 12 L 0.0720 0.8359 0.0921 13 L 0.0785 0.8381 0.0834 14 F 0.1005 0.8179 0.0816 15 Q 0.1032 0.8056 0.0912 16 M 0.1078 0.7719 0.1202 17 V 0.0941 0.7012 0.2047 18 G 0.0744 0.5654 0.3602 19 N 0.0742 0.5333 0.3925 20 A 0.0966 0.5827 0.3207 21 I 0.1354 0.4880 0.3767 22 N 0.1211 0.3571 0.5217 23 R 0.0440 0.4897 0.4664 24 N 0.0563 0.3937 0.5501 25 T 0.0554 0.5176 0.4271 26 Q 0.0728 0.6497 0.2775 27 Q 0.1269 0.6586 0.2144 28 L 0.1311 0.6563 0.2127 29 T 0.1182 0.6244 0.2574 30 Q 0.0863 0.6650 0.2487 31 D 0.0857 0.6326 0.2818 32 L 0.0618 0.6676 0.2707 33 R 0.0730 0.5008 0.4262 34 A 0.0951 0.3675 0.5375 35 M 0.0940 0.0618 0.8442 36 P 0.0544 0.1382 0.8074 37 N 0.0838 0.1147 0.8015 38 W 0.2175 0.1042 0.6783 39 S 0.4267 0.0581 0.5152 40 L 0.7047 0.0305 0.2648 41 R 0.7871 0.0245 0.1884 42 F 0.8964 0.0085 0.0950 43 V 0.9097 0.0088 0.0815 44 Y 0.9128 0.0085 0.0787 45 I 0.9009 0.0113 0.0878 46 V 0.8216 0.0191 0.1592 47 D 0.5793 0.0228 0.3979 48 R 0.0933 0.1816 0.7251 49 N 0.0703 0.1293 0.8004 50 N 0.0758 0.2069 0.7173 51 Q 0.0655 0.3994 0.5351 52 D 0.1753 0.4455 0.3792 53 L 0.1670 0.5616 0.2713 54 L 0.2614 0.3771 0.3615 55 K 0.2358 0.2656 0.4986 56 R 0.1604 0.0505 0.7890 57 P 0.1513 0.0380 0.8107 58 L 0.1070 0.0202 0.8728 59 P 0.0711 0.0237 0.9052 60 P 0.0473 0.1510 0.8017 61 G 0.1169 0.1424 0.7407 62 I 0.5744 0.0962 0.3294 63 M 0.7906 0.0499 0.1595 64 V 0.8125 0.0427 0.1448 65 L 0.6565 0.0692 0.2743 66 A 0.3055 0.0690 0.6255 67 P 0.1578 0.2326 0.6096 68 R 0.1739 0.2912 0.5349 69 L 0.2347 0.2471 0.5182 70 T 0.2071 0.2128 0.5801 71 A 0.1786 0.1809 0.6405 72 K 0.1402 0.1376 0.7223 73 H 0.1062 0.0319 0.8619 74 P 0.0714 0.1421 0.7865 75 Y 0.0701 0.2862 0.6437 76 D 0.0785 0.3847 0.5368 77 K 0.1262 0.4609 0.4129 78 V 0.2054 0.4709 0.3237 79 Q 0.2291 0.4285 0.3424 80 D 0.1514 0.4309 0.4177 81 R 0.0975 0.4378 0.4648 82 N 0.0955 0.3170 0.5875 83 R 0.1516 0.2957 0.5527 84 K 0.3040 0.2745 0.4214 85 L 0.4293 0.2135 0.3573 86 Y 0.3804 0.1115 0.5081 87 G 0.3170 0.0701 0.6128 88 R 0.4657 0.0523 0.4820 89 H 0.6839 0.0303 0.2859 90 I 0.7720 0.0137 0.2144 91 T 0.7635 0.0122 0.2243 92 L 0.5673 0.0437 0.3890 93 N 0.2813 0.0514 0.6672 94 D 0.1184 0.0581 0.8235 95 G 0.0864 0.0584 0.8552 96 N 0.1794 0.0418 0.7788 97 S 0.5279 0.0186 0.4535 98 V 0.7618 0.0053 0.2329 99 K 0.8658 0.0040 0.1302 100 V 0.9039 0.0036 0.0925 101 V 0.9001 0.0048 0.0951 102 T 0.8924 0.0048 0.1029 103 I 0.7960 0.0133 0.1907 104 S 0.5817 0.0272 0.3911 105 A 0.2833 0.0820 0.6347 106 G 0.1351 0.0690 0.7958 107 R 0.1449 0.0898 0.7653 108 D 0.1208 0.0925 0.7867 109 E 0.0877 0.0930 0.8193 110 G 0.0612 0.0382 0.9005 111 P 0.0571 0.1043 0.8386 112 D 0.0721 0.2329 0.6950 113 R 0.0368 0.6390 0.3241 114 D 0.0329 0.8079 0.1592 115 I 0.0375 0.8926 0.0699 116 I 0.0284 0.9179 0.0538 117 W 0.0240 0.9274 0.0486 118 E 0.0203 0.9323 0.0474 119 M 0.0232 0.9222 0.0546 120 F 0.0248 0.9043 0.0709 121 L 0.0199 0.8988 0.0813 122 E 0.0203 0.8323 0.1474 123 N 0.0256 0.6185 0.3559 124 L 0.0514 0.4162 0.5324 125 E 0.0313 0.1173 0.8514