# This file is the result of combining several RDB files, specifically # T0615.t06.str2.rdb (weight 1.54425) # T0615.t06.str4.rdb (weight 0.924988) # T0615.t06.pb.rdb (weight 0.789901) # T0615.t06.bys.rdb (weight 0.748322) # T0615.t06.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 T0615.t06.str2.rdb # ============================================ # TARGET T0615 # Using neural net dunbrack-40pc-3157-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 T0615.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 329.405 # # ============================================ # Comments from T0615.t06.str4.rdb # ============================================ # TARGET T0615 # Using neural net dunbrack-40pc-3157-t06-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 T0615.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 329.405 # # ============================================ # Comments from T0615.t06.pb.rdb # ============================================ # TARGET T0615 # Using neural net dunbrack-40pc-3157-t06-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 T0615.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 329.405 # # ============================================ # Comments from T0615.t06.bys.rdb # ============================================ # TARGET T0615 # Using neural net dunbrack-40pc-3157-t06-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 T0615.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 329.405 # # ============================================ # Comments from T0615.t06.alpha.rdb # ============================================ # TARGET T0615 # Using neural net dunbrack-40pc-3157-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 T0615.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 329.405 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2065 0.0884 0.7051 2 A 0.1664 0.1054 0.7282 3 T 0.1249 0.2488 0.6263 4 Y 0.1666 0.2162 0.6173 5 P 0.1100 0.3301 0.5599 6 S 0.0209 0.7507 0.2283 7 A 0.0097 0.8739 0.1164 8 K 0.0088 0.9131 0.0781 9 F 0.0084 0.9195 0.0722 10 M 0.0083 0.9206 0.0711 11 E 0.0083 0.9245 0.0672 12 C 0.0083 0.9236 0.0681 13 L 0.0083 0.9232 0.0685 14 Q 0.0083 0.9235 0.0682 15 Y 0.0084 0.9214 0.0703 16 A 0.0084 0.9194 0.0723 17 A 0.0085 0.9115 0.0800 18 F 0.0093 0.8886 0.1021 19 K 0.0144 0.8389 0.1467 20 H 0.0353 0.6738 0.2909 21 R 0.0326 0.5608 0.4066 22 Q 0.0430 0.3986 0.5584 23 Q 0.1717 0.3071 0.5213 24 R 0.2755 0.1986 0.5260 25 R 0.2806 0.1382 0.5812 26 K 0.2655 0.1549 0.5796 27 D 0.2098 0.0460 0.7442 28 P 0.0377 0.3991 0.5632 29 Q 0.0625 0.2190 0.7185 30 E 0.0646 0.1187 0.8167 31 T 0.2507 0.0347 0.7146 32 P 0.3739 0.0610 0.5651 33 Y 0.5055 0.0977 0.3968 34 V 0.5172 0.1317 0.3511 35 N 0.4073 0.2076 0.3851 36 H 0.2961 0.2814 0.4224 37 V 0.0544 0.7256 0.2200 38 I 0.0146 0.8571 0.1282 39 N 0.0091 0.9177 0.0732 40 V 0.0084 0.9222 0.0694 41 S 0.0083 0.9227 0.0690 42 T 0.0083 0.9234 0.0683 43 I 0.0086 0.9196 0.0719 44 L 0.0100 0.8955 0.0945 45 S 0.0131 0.8527 0.1343 46 V 0.0202 0.7701 0.2097 47 E 0.0418 0.5513 0.4068 48 A 0.0703 0.3307 0.5989 49 C 0.0864 0.2772 0.6364 50 I 0.1409 0.2393 0.6198 51 T 0.1648 0.1967 0.6385 52 D 0.1305 0.2110 0.6585 53 E 0.0172 0.7562 0.2266 54 G 0.0133 0.8559 0.1308 55 V 0.0141 0.9074 0.0785 56 L 0.0145 0.9083 0.0772 57 M 0.0180 0.9074 0.0746 58 A 0.0211 0.9052 0.0737 59 A 0.0215 0.9029 0.0756 60 L 0.0277 0.8794 0.0929 61 L 0.0359 0.8109 0.1532 62 H 0.0658 0.6711 0.2630 63 D 0.0671 0.5966 0.3362 64 V 0.0879 0.6118 0.3002 65 V 0.1294 0.5709 0.2997 66 E 0.1591 0.3778 0.4631 67 D 0.1430 0.2258 0.6311 68 T 0.1135 0.2188 0.6677 69 D 0.1168 0.1900 0.6932 70 A 0.1871 0.1244 0.6885 71 S 0.1807 0.0655 0.7538 72 F 0.0131 0.7449 0.2420 73 E 0.0096 0.8648 0.1256 74 D 0.0087 0.9183 0.0730 75 V 0.0088 0.9157 0.0755 76 E 0.0089 0.8970 0.0942 77 K 0.0094 0.8759 0.1147 78 L 0.0192 0.7579 0.2229 79 F 0.0593 0.4492 0.4915 80 G 0.0585 0.3167 0.6248 81 P 0.0142 0.6826 0.3032 82 D 0.0123 0.8178 0.1699 83 V 0.0124 0.9002 0.0874 84 C 0.0095 0.9111 0.0794 85 G 0.0102 0.9080 0.0818 86 L 0.0132 0.9032 0.0836 87 V 0.0207 0.8796 0.0997 88 R 0.0190 0.8469 0.1341 89 E 0.0337 0.7309 0.2353 90 V 0.0979 0.5617 0.3404 91 T 0.1235 0.4172 0.4593 92 D 0.0933 0.4061 0.5005 93 D 0.0721 0.4364 0.4915 94 K 0.0462 0.5163 0.4374 95 S 0.0779 0.4325 0.4896 96 L 0.1217 0.3898 0.4884 97 E 0.0878 0.4540 0.4582 98 K 0.0547 0.6452 0.3001 99 Q 0.0354 0.7665 0.1982 100 E 0.0266 0.8251 0.1483 101 R 0.0199 0.8690 0.1111 102 K 0.0111 0.8998 0.0891 103 R 0.0109 0.9045 0.0846 104 L 0.0122 0.9092 0.0785 105 Q 0.0124 0.9053 0.0823 106 I 0.0104 0.9096 0.0799 107 E 0.0099 0.8911 0.0990 108 N 0.0154 0.8156 0.1690 109 A 0.0211 0.8140 0.1649 110 A 0.0214 0.7506 0.2280 111 K 0.0419 0.5423 0.4158 112 S 0.1107 0.2974 0.5918 113 S 0.1423 0.1373 0.7204 114 C 0.2300 0.1276 0.6424 115 R 0.4147 0.0764 0.5088 116 A 0.6728 0.0465 0.2806 117 K 0.6977 0.0474 0.2549 118 L 0.7309 0.0429 0.2262 119 I 0.6961 0.0866 0.2174 120 K 0.4811 0.2421 0.2768 121 L 0.1676 0.5553 0.2772 122 A 0.0623 0.7180 0.2197 123 D 0.0285 0.7722 0.1993 124 K 0.0203 0.7757 0.2039 125 L 0.0322 0.7452 0.2227 126 D 0.0293 0.6880 0.2826 127 N 0.0476 0.5634 0.3890 128 L 0.0742 0.5793 0.3464 129 R 0.0760 0.6374 0.2866 130 D 0.1119 0.5531 0.3350 131 L 0.1091 0.5501 0.3408 132 Q 0.1222 0.4553 0.4225 133 V 0.1800 0.3170 0.5030 134 N 0.1914 0.1473 0.6613 135 T 0.1796 0.0548 0.7656 136 P 0.0532 0.3924 0.5543 137 T 0.0491 0.4314 0.5195 138 G 0.0546 0.5034 0.4420 139 W 0.0606 0.6833 0.2560 140 T 0.0492 0.7982 0.1526 141 Q 0.0254 0.8582 0.1165 142 E 0.0200 0.8807 0.0993 143 R 0.0185 0.8802 0.1012 144 R 0.0151 0.8857 0.0992 145 D 0.0108 0.8977 0.0916 146 Q 0.0127 0.8926 0.0947 147 Y 0.0146 0.8853 0.1001 148 F 0.0120 0.8983 0.0897 149 V 0.0138 0.8949 0.0912 150 W 0.0188 0.8782 0.1029 151 A 0.0248 0.8361 0.1392 152 K 0.0364 0.8032 0.1604 153 K 0.0248 0.7964 0.1788 154 V 0.0215 0.7487 0.2299 155 V 0.0352 0.6817 0.2831 156 D 0.0369 0.5803 0.3828 157 N 0.0478 0.4441 0.5081 158 L 0.0840 0.4767 0.4393 159 R 0.0556 0.5686 0.3758 160 G 0.0724 0.4832 0.4443 161 T 0.0970 0.5262 0.3768 162 N 0.0671 0.6508 0.2820 163 A 0.0430 0.7829 0.1742 164 N 0.0281 0.8416 0.1303 165 L 0.0181 0.8769 0.1050 166 E 0.0151 0.8848 0.1002 167 L 0.0143 0.8825 0.1032 168 K 0.0163 0.8578 0.1259 169 L 0.0180 0.8565 0.1255 170 D 0.0158 0.8660 0.1182 171 E 0.0105 0.8822 0.1073 172 I 0.0117 0.8658 0.1225 173 F 0.0147 0.8683 0.1170 174 R 0.0205 0.8443 0.1353 175 Q 0.0344 0.7678 0.1979 176 R 0.0563 0.5924 0.3513 177 G 0.0507 0.4714 0.4779 178 L 0.1202 0.4083 0.4715 179 L 0.1694 0.2653 0.5652