# This file is the result of combining several RDB files, specifically # T0615.t04.str2.rdb (weight 1.54425) # T0615.t04.str4.rdb (weight 0.924988) # T0615.t04.pb.rdb (weight 0.789901) # T0615.t04.bys.rdb (weight 0.748322) # T0615.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 T0615.t04.str2.rdb # ============================================ # TARGET T0615 # 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 T0615.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 287.327 # # ============================================ # Comments from T0615.t04.str4.rdb # ============================================ # TARGET T0615 # 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 T0615.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 287.327 # # ============================================ # Comments from T0615.t04.pb.rdb # ============================================ # TARGET T0615 # 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 T0615.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 287.327 # # ============================================ # Comments from T0615.t04.bys.rdb # ============================================ # TARGET T0615 # 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 T0615.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 287.327 # # ============================================ # Comments from T0615.t04.alpha.rdb # ============================================ # TARGET T0615 # 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 T0615.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 287.327 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2057 0.0939 0.7004 2 A 0.1709 0.1037 0.7254 3 T 0.1417 0.2321 0.6262 4 Y 0.1777 0.1570 0.6654 5 P 0.1203 0.2880 0.5917 6 S 0.0216 0.7348 0.2435 7 A 0.0110 0.8615 0.1275 8 K 0.0094 0.9098 0.0808 9 F 0.0084 0.9184 0.0733 10 M 0.0083 0.9225 0.0692 11 E 0.0083 0.9242 0.0675 12 C 0.0083 0.9241 0.0676 13 L 0.0083 0.9239 0.0679 14 Q 0.0083 0.9242 0.0676 15 Y 0.0083 0.9223 0.0695 16 A 0.0084 0.9164 0.0752 17 A 0.0084 0.9143 0.0773 18 F 0.0090 0.8968 0.0942 19 K 0.0166 0.8104 0.1730 20 H 0.0363 0.6636 0.3001 21 R 0.0411 0.5660 0.3929 22 Q 0.0492 0.4406 0.5102 23 Q 0.1337 0.3910 0.4753 24 R 0.2668 0.2610 0.4722 25 R 0.2432 0.2182 0.5386 26 K 0.1894 0.2340 0.5766 27 D 0.1838 0.1083 0.7079 28 P 0.0560 0.3483 0.5956 29 Q 0.0810 0.3442 0.5748 30 E 0.1532 0.1824 0.6644 31 T 0.2406 0.0688 0.6907 32 P 0.2376 0.1631 0.5992 33 Y 0.3335 0.2415 0.4250 34 V 0.2724 0.3907 0.3369 35 N 0.1686 0.5006 0.3308 36 H 0.1514 0.5603 0.2883 37 V 0.0201 0.8391 0.1407 38 I 0.0114 0.8901 0.0985 39 N 0.0101 0.9195 0.0704 40 V 0.0093 0.9209 0.0698 41 S 0.0085 0.9227 0.0688 42 T 0.0088 0.9225 0.0688 43 I 0.0089 0.9178 0.0733 44 L 0.0100 0.9081 0.0820 45 S 0.0132 0.8695 0.1173 46 V 0.0158 0.8444 0.1398 47 E 0.0367 0.6461 0.3172 48 A 0.0769 0.3531 0.5699 49 C 0.1035 0.2115 0.6850 50 I 0.1356 0.2207 0.6437 51 T 0.1285 0.2357 0.6357 52 D 0.1336 0.2584 0.6080 53 E 0.0132 0.7413 0.2456 54 G 0.0123 0.8572 0.1305 55 V 0.0177 0.9063 0.0760 56 L 0.0142 0.9149 0.0709 57 M 0.0153 0.9149 0.0698 58 A 0.0145 0.9149 0.0706 59 A 0.0186 0.9011 0.0803 60 L 0.0262 0.8531 0.1207 61 L 0.0394 0.7332 0.2274 62 H 0.0701 0.5718 0.3581 63 D 0.0837 0.4918 0.4245 64 V 0.1118 0.4697 0.4185 65 V 0.1636 0.4213 0.4151 66 E 0.1707 0.4192 0.4101 67 D 0.1319 0.2661 0.6020 68 T 0.1202 0.2018 0.6780 69 D 0.1315 0.1746 0.6940 70 A 0.1908 0.1095 0.6997 71 S 0.1799 0.0392 0.7809 72 F 0.0149 0.7296 0.2555 73 E 0.0096 0.8647 0.1257 74 D 0.0089 0.9115 0.0796 75 V 0.0087 0.9074 0.0839 76 E 0.0091 0.9046 0.0864 77 K 0.0101 0.8799 0.1101 78 L 0.0167 0.7328 0.2505 79 F 0.0568 0.3841 0.5590 80 G 0.0748 0.3767 0.5484 81 P 0.0166 0.7239 0.2595 82 D 0.0155 0.8068 0.1777 83 V 0.0139 0.8707 0.1154 84 C 0.0110 0.8997 0.0892 85 G 0.0126 0.8893 0.0980 86 L 0.0129 0.8998 0.0872 87 V 0.0176 0.8802 0.1022 88 R 0.0163 0.8649 0.1188 89 E 0.0309 0.7923 0.1768 90 V 0.0690 0.6569 0.2741 91 T 0.1091 0.4257 0.4652 92 D 0.0777 0.4794 0.4429 93 D 0.0582 0.5281 0.4137 94 K 0.0445 0.5821 0.3734 95 S 0.0701 0.5382 0.3917 96 L 0.0919 0.5832 0.3249 97 E 0.0669 0.6411 0.2920 98 K 0.0368 0.7661 0.1971 99 Q 0.0336 0.7923 0.1741 100 E 0.0235 0.8297 0.1468 101 R 0.0188 0.8683 0.1129 102 K 0.0126 0.8928 0.0947 103 R 0.0110 0.9078 0.0812 104 L 0.0125 0.9096 0.0779 105 Q 0.0118 0.9116 0.0766 106 I 0.0112 0.9029 0.0859 107 E 0.0121 0.8878 0.1001 108 N 0.0246 0.7767 0.1986 109 A 0.0591 0.7060 0.2350 110 A 0.0934 0.5627 0.3439 111 K 0.1040 0.4080 0.4880 112 S 0.1418 0.2156 0.6426 113 S 0.1970 0.1045 0.6985 114 C 0.3123 0.0695 0.6182 115 R 0.4922 0.0477 0.4601 116 A 0.6874 0.0119 0.3007 117 K 0.7337 0.0141 0.2523 118 L 0.7624 0.0081 0.2295 119 I 0.7485 0.0298 0.2217 120 K 0.6310 0.0912 0.2778 121 L 0.3074 0.3321 0.3605 122 A 0.1361 0.5270 0.3369 123 D 0.0590 0.6104 0.3306 124 K 0.0407 0.6927 0.2666 125 L 0.0499 0.6377 0.3124 126 D 0.0449 0.5652 0.3899 127 N 0.0798 0.4468 0.4734 128 L 0.0831 0.4651 0.4518 129 R 0.1062 0.4795 0.4142 130 D 0.1440 0.4429 0.4130 131 L 0.1216 0.5041 0.3742 132 Q 0.1413 0.4337 0.4251 133 V 0.1635 0.3579 0.4786 134 N 0.1815 0.1705 0.6480 135 T 0.1601 0.0917 0.7482 136 P 0.0672 0.4060 0.5269 137 T 0.0780 0.3687 0.5533 138 G 0.0829 0.3516 0.5655 139 W 0.1123 0.4683 0.4194 140 T 0.0947 0.6362 0.2691 141 Q 0.0596 0.7745 0.1658 142 E 0.0498 0.8127 0.1375 143 R 0.0417 0.8189 0.1394 144 R 0.0232 0.8470 0.1298 145 D 0.0172 0.8741 0.1086 146 Q 0.0202 0.8592 0.1206 147 Y 0.0219 0.8487 0.1294 148 F 0.0145 0.8842 0.1013 149 V 0.0090 0.9030 0.0880 150 W 0.0087 0.9036 0.0877 151 A 0.0086 0.9048 0.0866 152 K 0.0085 0.9038 0.0877 153 K 0.0085 0.9008 0.0907 154 V 0.0090 0.8970 0.0940 155 V 0.0089 0.8843 0.1069 156 D 0.0090 0.8686 0.1223 157 N 0.0124 0.8314 0.1562 158 L 0.0261 0.7620 0.2119 159 R 0.0285 0.7301 0.2414 160 G 0.0395 0.6798 0.2807 161 T 0.0518 0.6745 0.2737 162 N 0.0601 0.6482 0.2917 163 A 0.0290 0.7400 0.2310 164 N 0.0428 0.6961 0.2611 165 L 0.0269 0.7563 0.2168 166 E 0.0221 0.8124 0.1655 167 L 0.0238 0.8302 0.1460 168 K 0.0378 0.7700 0.1923 169 L 0.0148 0.8537 0.1314 170 D 0.0088 0.9019 0.0892 171 E 0.0085 0.9176 0.0738 172 I 0.0086 0.9155 0.0759 173 F 0.0086 0.9158 0.0757 174 R 0.0088 0.8995 0.0917 175 Q 0.0121 0.8318 0.1561 176 R 0.0502 0.6260 0.3238 177 G 0.0381 0.3909 0.5710 178 L 0.0907 0.3555 0.5538 179 L 0.1451 0.2330 0.6219