# This file is the result of combining several RDB files, specifically # T0396.t04.str2.rdb (weight 1.54425) # T0396.t04.str4.rdb (weight 0.924988) # T0396.t04.pb.rdb (weight 0.789901) # T0396.t04.bys.rdb (weight 0.748322) # T0396.t04.alpha.rdb (weight 0.678173) # 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 T0396.t04.str2.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t04-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 T0396.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 106.089 # # ============================================ # Comments from T0396.t04.str4.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0396.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 106.089 # # ============================================ # Comments from T0396.t04.pb.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0396.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 106.089 # # ============================================ # Comments from T0396.t04.bys.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0396.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 106.089 # # ============================================ # Comments from T0396.t04.alpha.rdb # ============================================ # TARGET T0396 # Using neural net dunbrack-40pc-3157-t04-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 T0396.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 106.089 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1830 0.0833 0.7337 2 S 0.2012 0.0949 0.7039 3 M 0.1376 0.3418 0.5206 4 L 0.1338 0.4216 0.4446 5 H 0.1703 0.3352 0.4945 6 W 0.1672 0.2618 0.5710 7 G 0.1270 0.2309 0.6421 8 P 0.0327 0.6791 0.2882 9 K 0.0207 0.8203 0.1590 10 Y 0.0173 0.8937 0.0890 11 W 0.0122 0.9143 0.0735 12 R 0.0103 0.9208 0.0690 13 S 0.0101 0.9210 0.0689 14 L 0.0096 0.9214 0.0690 15 H 0.0104 0.9196 0.0700 16 L 0.0126 0.9133 0.0741 17 Y 0.0247 0.8877 0.0876 18 A 0.0670 0.8103 0.1227 19 I 0.1386 0.6829 0.1785 20 F 0.2277 0.4051 0.3672 21 F 0.2266 0.1933 0.5801 22 S 0.1153 0.2488 0.6359 23 D 0.1023 0.1965 0.7012 24 A 0.1912 0.0747 0.7341 25 P 0.1591 0.1662 0.6747 26 S 0.1605 0.1468 0.6927 27 W 0.0380 0.5933 0.3687 28 K 0.0269 0.7407 0.2324 29 E 0.0336 0.8187 0.1478 30 K 0.0141 0.8786 0.1073 31 Y 0.0100 0.8995 0.0905 32 E 0.0086 0.9216 0.0698 33 A 0.0083 0.9231 0.0686 34 I 0.0083 0.9241 0.0676 35 Q 0.0083 0.9247 0.0670 36 W 0.0083 0.9246 0.0671 37 I 0.0083 0.9230 0.0687 38 L 0.0084 0.9206 0.0710 39 N 0.0090 0.9019 0.0891 40 F 0.0131 0.8515 0.1354 41 I 0.0185 0.8175 0.1641 42 E 0.0322 0.7390 0.2288 43 S 0.0809 0.4694 0.4497 44 L 0.1887 0.1684 0.6429 45 P 0.1221 0.1992 0.6787 46 C 0.0914 0.4079 0.5007 47 T 0.0197 0.7130 0.2672 48 R 0.0186 0.7823 0.1991 49 C 0.0215 0.8435 0.1350 50 Q 0.0103 0.8887 0.1011 51 H 0.0089 0.9115 0.0795 52 H 0.0098 0.9082 0.0820 53 A 0.0089 0.9100 0.0811 54 F 0.0085 0.9158 0.0757 55 S 0.0085 0.9135 0.0780 56 Y 0.0097 0.8852 0.1051 57 L 0.0164 0.8458 0.1378 58 T 0.0244 0.7319 0.2437 59 K 0.0613 0.4188 0.5198 60 N 0.1775 0.0805 0.7420 61 P 0.1269 0.2297 0.6434 62 L 0.1726 0.2383 0.5891 63 T 0.2541 0.1607 0.5852 64 L 0.2672 0.1589 0.5739 65 N 0.1944 0.1488 0.6568 66 N 0.1748 0.0851 0.7401 67 S 0.0525 0.5350 0.4125 68 E 0.0177 0.7685 0.2139 69 D 0.0227 0.8293 0.1480 70 F 0.0336 0.8555 0.1109 71 Q 0.0214 0.8892 0.0894 72 Y 0.0230 0.8944 0.0826 73 W 0.0287 0.8853 0.0860 74 T 0.0346 0.8689 0.0965 75 F 0.0290 0.8762 0.0948 76 A 0.0256 0.8645 0.1099 77 F 0.0276 0.8083 0.1641 78 H 0.0370 0.7114 0.2516 79 N 0.0338 0.7032 0.2630 80 N 0.0354 0.7285 0.2362 81 V 0.0756 0.6793 0.2451 82 N 0.0839 0.5895 0.3267 83 N 0.0415 0.6813 0.2772 84 R 0.0740 0.5789 0.3471 85 L 0.1075 0.3420 0.5505 86 N 0.0843 0.1735 0.7422 87 K 0.1812 0.1207 0.6981 88 K 0.2294 0.1431 0.6275 89 I 0.2977 0.1932 0.5091 90 I 0.3607 0.1033 0.5360 91 S 0.2347 0.0327 0.7325 92 W 0.0484 0.5153 0.4363 93 S 0.0374 0.6449 0.3177 94 E 0.0796 0.6600 0.2604 95 Y 0.0968 0.6509 0.2522 96 K 0.0756 0.6827 0.2417 97 N 0.1580 0.5688 0.2732 98 I 0.2035 0.4200 0.3765 99 Y 0.2319 0.2594 0.5087 100 E 0.1653 0.3078 0.5268 101 Q 0.1085 0.4189 0.4726 102 S 0.1136 0.3658 0.5205 103 I 0.1673 0.2738 0.5589 104 L 0.1808 0.1993 0.6198 105 K 0.1672 0.1432 0.6896