# This file is the result of combining several RDB files, specifically # T0366.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0366.t2k.stride-ebghtl.rdb (weight 1.24869) # T0366.t2k.str2.rdb (weight 1.54758) # T0366.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 T0366.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1382 # # ============================================ # Comments from T0366.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1382 # # ============================================ # Comments from T0366.t2k.str2.rdb # ============================================ # TARGET T0366 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0366.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 1382 # # ============================================ # Comments from T0366.t2k.alpha.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1382 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.3087 0.1199 0.5714 2 E 0.3457 0.1637 0.4906 3 N 0.3248 0.1849 0.4903 4 L 0.2519 0.1900 0.5581 5 Y 0.2535 0.1481 0.5985 6 F 0.2933 0.1430 0.5638 7 Q 0.2494 0.1133 0.6373 8 S 0.1715 0.0990 0.7295 9 M 0.0935 0.1135 0.7931 10 G 0.1115 0.0655 0.8230 11 L 0.2867 0.0197 0.6936 12 R 0.5798 0.0100 0.4102 13 T 0.8380 0.0059 0.1561 14 V 0.8979 0.0044 0.0977 15 E 0.9103 0.0040 0.0857 16 M 0.9069 0.0043 0.0888 17 K 0.8588 0.0070 0.1342 18 K 0.7052 0.0205 0.2743 19 G 0.2909 0.0271 0.6820 20 P 0.0752 0.0730 0.8518 21 T 0.0660 0.0711 0.8629 22 D 0.1284 0.0504 0.8212 23 S 0.2742 0.0524 0.6734 24 L 0.6077 0.0198 0.3724 25 G 0.8084 0.0118 0.1798 26 I 0.8792 0.0059 0.1149 27 S 0.8955 0.0043 0.1002 28 I 0.8872 0.0074 0.1054 29 A 0.7832 0.0206 0.1962 30 G 0.4866 0.0264 0.4870 31 G 0.2167 0.0511 0.7322 32 V 0.1754 0.0844 0.7402 33 G 0.1381 0.0910 0.7709 34 S 0.1066 0.0943 0.7992 35 P 0.0788 0.1410 0.7802 36 L 0.0735 0.1321 0.7944 37 G 0.1018 0.0967 0.8015 38 D 0.1672 0.0599 0.7728 39 V 0.2738 0.0408 0.6854 40 P 0.5306 0.0188 0.4506 41 I 0.8459 0.0066 0.1475 42 F 0.8991 0.0053 0.0955 43 I 0.8956 0.0052 0.0992 44 A 0.8326 0.0293 0.1381 45 M 0.7862 0.0099 0.2039 46 M 0.6531 0.0161 0.3308 47 H 0.2530 0.0199 0.7271 48 P 0.0484 0.0846 0.8670 49 T 0.0315 0.0492 0.9193 50 G 0.0804 0.1027 0.8170 51 V 0.0642 0.6133 0.3225 52 A 0.0437 0.7379 0.2184 53 A 0.0276 0.7834 0.1889 54 Q 0.0361 0.7142 0.2497 55 T 0.0656 0.2713 0.6630 56 Q 0.0342 0.0671 0.8987 57 K 0.1346 0.0420 0.8235 58 L 0.3752 0.0169 0.6079 59 R 0.1087 0.0199 0.8713 60 V 0.0586 0.1154 0.8259 61 G 0.0802 0.0597 0.8602 62 D 0.3765 0.0479 0.5756 63 R 0.8201 0.0104 0.1695 64 I 0.9003 0.0075 0.0921 65 V 0.9066 0.0069 0.0864 66 T 0.8998 0.0087 0.0915 67 I 0.8202 0.0185 0.1613 68 C 0.1552 0.0296 0.8152 69 G 0.0594 0.0499 0.8906 70 T 0.5277 0.0233 0.4490 71 S 0.5528 0.0254 0.4218 72 T 0.4139 0.1138 0.4723 73 E 0.1876 0.1526 0.6598 74 G 0.0914 0.1047 0.8040 75 M 0.1874 0.0387 0.7739 76 T 0.1654 0.0439 0.7907 77 H 0.0057 0.9209 0.0734 78 T 0.0048 0.9540 0.0412 79 Q 0.0047 0.9578 0.0375 80 A 0.0047 0.9594 0.0359 81 V 0.0047 0.9592 0.0361 82 N 0.0047 0.9569 0.0384 83 L 0.0048 0.9526 0.0426 84 L 0.0056 0.9365 0.0579 85 K 0.0072 0.8691 0.1237 86 N 0.0171 0.6100 0.3729 87 A 0.0581 0.1800 0.7619 88 S 0.0353 0.0848 0.8799 89 G 0.0392 0.0597 0.9011 90 S 0.2741 0.0214 0.7045 91 I 0.7607 0.0045 0.2349 92 E 0.9046 0.0036 0.0918 93 M 0.9205 0.0033 0.0762 94 Q 0.9182 0.0034 0.0784 95 V 0.9051 0.0033 0.0916 96 V 0.8387 0.0045 0.1568 97 A 0.6163 0.0080 0.3756 98 G 0.2169 0.0246 0.7585 99 G 0.0732 0.0822 0.8446 100 D 0.0762 0.0742 0.8496 101 V 0.1153 0.0594 0.8252 102 S 0.1226 0.0660 0.8114 103 E 0.1100 0.1225 0.7675 104 T 0.0862 0.1236 0.7902 105 S 0.1192 0.1011 0.7797 106 V 0.0632 0.0477 0.8891