# This file is the result of combining several RDB files, specifically # T0372.t04.dssp-ebghstl.rdb (weight 1.53986) # T0372.t04.stride-ebghtl.rdb (weight 1.24869) # T0372.t04.str2.rdb (weight 1.54758) # T0372.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 T0372.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t04.stride-ebghtl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t04.str2.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ # Comments from T0372.t04.alpha.rdb # ============================================ # TARGET T0372 # 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 T0372.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 23 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0927 0.0382 0.8691 2 I 0.1529 0.0270 0.8201 3 P 0.1803 0.0363 0.7834 4 F 0.1926 0.0476 0.7598 5 K 0.2201 0.0425 0.7374 6 D 0.2704 0.0269 0.7027 7 I 0.2667 0.0118 0.7215 8 T 0.3312 0.0111 0.6577 9 L 0.0829 0.5622 0.3548 10 A 0.0562 0.4648 0.4789 11 D 0.0863 0.4068 0.5069 12 R 0.0120 0.8702 0.1177 13 D 0.0066 0.8999 0.0935 14 T 0.0081 0.9066 0.0854 15 I 0.0132 0.9058 0.0811 16 T 0.0108 0.9145 0.0747 17 A 0.0094 0.9089 0.0816 18 F 0.0114 0.8829 0.1056 19 T 0.0271 0.7894 0.1835 20 M 0.0275 0.6568 0.3157 21 K 0.0329 0.4481 0.5190 22 S 0.0610 0.2169 0.7221 23 D 0.0582 0.1581 0.7837 24 R 0.0823 0.2431 0.6747 25 R 0.1433 0.2795 0.5772 26 N 0.1808 0.2800 0.5392 27 C 0.1786 0.2447 0.5767 28 D 0.1483 0.3660 0.4858 29 L 0.1903 0.4040 0.4058 30 S 0.1972 0.4451 0.3578 31 F 0.1160 0.6845 0.1995 32 S 0.0820 0.7260 0.1921 33 N 0.0693 0.7810 0.1497 34 L 0.0728 0.8219 0.1053 35 C 0.0939 0.8057 0.1004 36 S 0.1115 0.7551 0.1334 37 W 0.1245 0.6687 0.2069 38 R 0.1254 0.5532 0.3214 39 F 0.1271 0.4248 0.4482 40 L 0.2035 0.3063 0.4902 41 Y 0.2537 0.1369 0.6094 42 D 0.2941 0.0611 0.6448 43 T 0.6293 0.0234 0.3473 44 Q 0.8199 0.0159 0.1642 45 F 0.9040 0.0078 0.0882 46 A 0.9005 0.0061 0.0934 47 V 0.9133 0.0045 0.0822 48 I 0.7987 0.0164 0.1848 49 D 0.2558 0.0540 0.6902 50 D 0.1549 0.0443 0.8008 51 F 0.7856 0.0084 0.2060 52 L 0.9168 0.0032 0.0800 53 V 0.9272 0.0035 0.0693 54 F 0.9241 0.0039 0.0720 55 K 0.9018 0.0107 0.0875 56 F 0.8833 0.0059 0.1108 57 W 0.7705 0.0127 0.2169 58 A 0.4165 0.0330 0.5505 59 G 0.0597 0.0352 0.9052 60 E 0.0958 0.0494 0.8547 61 Q 0.5439 0.0236 0.4325 62 L 0.7302 0.0138 0.2560 63 A 0.8253 0.0161 0.1586 64 Y 0.8617 0.0123 0.1260 65 M 0.7529 0.0151 0.2320 66 M 0.5070 0.0169 0.4760 67 P 0.3234 0.0281 0.6486 68 V 0.1747 0.0423 0.7830 69 G 0.0880 0.0349 0.8771 70 N 0.0531 0.1334 0.8135 71 G 0.0435 0.1259 0.8305 72 D 0.0978 0.1478 0.7544 73 L 0.0073 0.9234 0.0693 74 K 0.0047 0.9573 0.0380 75 A 0.0047 0.9594 0.0359 76 V 0.0047 0.9581 0.0372 77 L 0.0047 0.9598 0.0355 78 R 0.0047 0.9609 0.0345 79 K 0.0047 0.9588 0.0366 80 L 0.0047 0.9538 0.0415 81 I 0.0048 0.9498 0.0454 82 E 0.0052 0.9330 0.0617 83 D 0.0072 0.8946 0.0982 84 A 0.0079 0.8698 0.1223 85 D 0.0110 0.7752 0.2139 86 K 0.0117 0.7012 0.2871 87 E 0.0260 0.4744 0.4996 88 K 0.0318 0.2171 0.7512 89 H 0.0757 0.1029 0.8214 90 N 0.1273 0.0955 0.7773 91 F 0.3980 0.0807 0.5213 92 C 0.5770 0.0826 0.3404 93 M 0.6307 0.1388 0.2305 94 L 0.4458 0.2096 0.3446 95 G 0.3246 0.1330 0.5424 96 V 0.2300 0.0865 0.6835 97 C 0.1115 0.1191 0.7694 98 S 0.0110 0.8186 0.1704 99 N 0.0093 0.8424 0.1483 100 M 0.0078 0.9001 0.0921 101 R 0.0076 0.9273 0.0651 102 A 0.0065 0.9261 0.0674 103 D 0.0059 0.9299 0.0641 104 L 0.0062 0.9270 0.0668 105 E 0.0068 0.9181 0.0750 106 A 0.0092 0.8744 0.1164 107 I 0.0243 0.7178 0.2578 108 L 0.0916 0.0808 0.8275 109 P 0.0326 0.1808 0.7866 110 E 0.0225 0.1654 0.8121 111 R 0.1846 0.1462 0.6692 112 F 0.5968 0.0262 0.3770 113 I 0.7945 0.0159 0.1897 114 F 0.8316 0.0128 0.1556 115 T 0.6802 0.0272 0.2926 116 E 0.4804 0.0780 0.4416 117 D 0.2536 0.1057 0.6407 118 R 0.1307 0.2888 0.5805 119 A 0.0980 0.2910 0.6110 120 Y 0.0851 0.3065 0.6084 121 A 0.0868 0.1903 0.7229 122 D 0.0833 0.1035 0.8131