# This file is the result of combining several RDB files, specifically # T0514.t04.dssp-ebghstl.rdb (weight 1.53986) # T0514.t04.stride-ebghtl.rdb (weight 1.24869) # T0514.t04.str2.rdb (weight 1.54758) # T0514.t04.alpha.rdb (weight 0.659012) # T0514.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0514.t2k.stride-ebghtl.rdb (weight 1.24869) # T0514.t2k.str2.rdb (weight 1.54758) # T0514.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 T0514.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0514 # Using neural net t04-2621-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 T0514.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 205 # # ============================================ # Comments from T0514.t04.stride-ebghtl.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t04.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t04.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0514 # 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 T0514.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 84 # # ============================================ # Comments from T0514.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0514 # 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 T0514.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 84 # # ============================================ # Comments from T0514.t2k.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 84 # # ============================================ # Comments from T0514.t2k.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 84 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0874 0.0911 0.8214 2 S 0.2561 0.1394 0.6045 3 L 0.3084 0.1295 0.5620 4 T 0.3351 0.1122 0.5527 5 E 0.4145 0.0891 0.4963 6 T 0.4106 0.0771 0.5123 7 Y 0.2616 0.0818 0.6565 8 G 0.1714 0.0681 0.7605 9 L 0.2579 0.0722 0.6700 10 W 0.5568 0.0475 0.3957 11 S 0.7758 0.0240 0.2003 12 I 0.8336 0.0233 0.1431 13 N 0.8244 0.0203 0.1553 14 C 0.7553 0.0233 0.2214 15 G 0.6149 0.0441 0.3410 16 I 0.3973 0.0440 0.5587 17 Q 0.1661 0.0609 0.7730 18 E 0.0549 0.1037 0.8414 19 G 0.0533 0.0891 0.8576 20 K 0.1764 0.0896 0.7340 21 K 0.3865 0.0831 0.5303 22 V 0.5926 0.1287 0.2787 23 C 0.6621 0.1488 0.1891 24 F 0.7231 0.1515 0.1254 25 M 0.7786 0.1175 0.1039 26 H 0.7661 0.1204 0.1134 27 R 0.7860 0.1020 0.1120 28 Q 0.7709 0.0990 0.1301 29 E 0.7436 0.1130 0.1434 30 V 0.6596 0.1194 0.2210 31 N 0.3036 0.1165 0.5799 32 D 0.0763 0.1189 0.8047 33 Q 0.0537 0.0541 0.8922 34 N 0.0638 0.0359 0.9004 35 R 0.3748 0.0085 0.6167 36 V 0.7895 0.0037 0.2068 37 V 0.8775 0.0067 0.1159 38 V 0.9158 0.0044 0.0799 39 A 0.9293 0.0031 0.0676 40 M 0.9295 0.0033 0.0673 41 S 0.9261 0.0035 0.0704 42 V 0.9178 0.0033 0.0789 43 V 0.8785 0.0071 0.1144 44 L 0.8305 0.0064 0.1631 45 N 0.4289 0.0241 0.5470 46 A 0.0680 0.0813 0.8508 47 D 0.0494 0.0394 0.9112 48 G 0.0930 0.0413 0.8657 49 V 0.3729 0.0147 0.6124 50 V 0.7434 0.0080 0.2486 51 S 0.8735 0.0057 0.1208 52 G 0.9156 0.0040 0.0803 53 N 0.9247 0.0036 0.0717 54 L 0.9231 0.0032 0.0737 55 T 0.8997 0.0037 0.0966 56 V 0.7489 0.0058 0.2452 57 P 0.4240 0.0194 0.5566 58 F 0.1282 0.1515 0.7202 59 G 0.1956 0.1735 0.6309 60 I 0.3850 0.1269 0.4881 61 L 0.5101 0.0675 0.4225 62 V 0.4447 0.0419 0.5133 63 S 0.1500 0.0619 0.7881 64 K 0.0547 0.1111 0.8341 65 P 0.1234 0.0608 0.8158 66 V 0.5555 0.0148 0.4298 67 R 0.8230 0.0079 0.1692 68 L 0.8871 0.0057 0.1072 69 Q 0.8656 0.0046 0.1298 70 V 0.7398 0.0124 0.2478 71 D 0.2530 0.0319 0.7151 72 E 0.0595 0.0892 0.8513 73 G 0.0499 0.1359 0.8142 74 K 0.0918 0.1407 0.7674 75 A 0.1483 0.1255 0.7262 76 V 0.1905 0.1190 0.6905 77 I 0.2867 0.1134 0.5999 78 E 0.3864 0.0801 0.5336 79 T 0.3938 0.0309 0.5752 80 G 0.4732 0.0316 0.4952 81 I 0.7034 0.0289 0.2677 82 R 0.7550 0.0365 0.2085 83 T 0.7581 0.0226 0.2193 84 C 0.5758 0.0243 0.3998 85 V 0.2915 0.0255 0.6830 86 P 0.1234 0.0703 0.8063 87 A 0.1305 0.0587 0.8108 88 G 0.3279 0.0444 0.6276 89 C 0.6117 0.0231 0.3652 90 I 0.8382 0.0139 0.1479 91 V 0.8511 0.0131 0.1358 92 P 0.8303 0.0199 0.1498 93 I 0.6970 0.0185 0.2844 94 V 0.4942 0.0220 0.4838 95 F 0.2208 0.0217 0.7575 96 D 0.0727 0.0199 0.9074 97 K 0.0053 0.9069 0.0878 98 N 0.0051 0.9394 0.0555 99 Y 0.0048 0.9521 0.0431 100 V 0.0047 0.9570 0.0383 101 A 0.0056 0.9500 0.0444 102 A 0.0057 0.9422 0.0522 103 L 0.0114 0.9132 0.0754 104 R 0.0119 0.8321 0.1560 105 A 0.0340 0.4685 0.4975 106 G 0.0369 0.0654 0.8977 107 K 0.0819 0.0445 0.8735 108 H 0.4105 0.0175 0.5721 109 L 0.7673 0.0077 0.2250 110 K 0.8977 0.0052 0.0971 111 L 0.9192 0.0036 0.0773 112 A 0.9077 0.0043 0.0880 113 M 0.8601 0.0051 0.1348 114 T 0.8157 0.0065 0.1778 115 I 0.6412 0.0113 0.3475 116 A 0.4406 0.0422 0.5172 117 A 0.2434 0.1215 0.6351 118 P 0.1555 0.1058 0.7387 119 G 0.0964 0.1013 0.8023 120 E 0.0623 0.1110 0.8267 121 P 0.0673 0.0765 0.8562 122 P 0.2372 0.0241 0.7387 123 L 0.4849 0.0111 0.5040 124 N 0.6958 0.0072 0.2970 125 D 0.7926 0.0089 0.1984 126 L 0.8252 0.0068 0.1680 127 F 0.8462 0.0062 0.1476 128 V 0.7576 0.0102 0.2322 129 Q 0.6357 0.0182 0.3461 130 L 0.2039 0.2866 0.5094 131 N 0.0605 0.3997 0.5397 132 G 0.0730 0.3607 0.5662 133 F 0.0265 0.7091 0.2644 134 S 0.0123 0.9028 0.0848 135 N 0.0071 0.9267 0.0662 136 A 0.0049 0.9428 0.0523 137 L 0.0051 0.9399 0.0551 138 N 0.0057 0.9015 0.0928 139 R 0.0063 0.8701 0.1236 140 L 0.0181 0.7861 0.1958 141 I 0.0103 0.7620 0.2277 142 A 0.0155 0.7289 0.2556 143 L 0.0340 0.5816 0.3844 144 Q 0.0534 0.3747 0.5720 145 K 0.0292 0.0694 0.9014