# This file is the result of combining several RDB files, specifically # T0231.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0231.t2k.stride-ebghtl.rdb (weight 1.24869) # T0231.t2k.str2.rdb (weight 1.54758) # T0231.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 T0231.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0231 # 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 T0231.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 142 # # ============================================ # Comments from T0231.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0231 # 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 T0231.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 142 # # ============================================ # Comments from T0231.t2k.str2.rdb # ============================================ # TARGET T0231 # 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 T0231.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 142 # # ============================================ # Comments from T0231.t2k.alpha.rdb # ============================================ # TARGET T0231 # 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 T0231.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 142 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1509 0.0735 0.7755 2 S 0.1874 0.1256 0.6870 3 D 0.1603 0.1552 0.6844 4 S 0.1267 0.2015 0.6718 5 L 0.1947 0.1110 0.6943 6 V 0.3140 0.0733 0.6126 7 V 0.4828 0.0490 0.4682 8 C 0.5060 0.0243 0.4697 9 E 0.4902 0.0150 0.4948 10 V 0.1954 0.0158 0.7889 11 D 0.0665 0.0153 0.9182 12 P 0.0051 0.9190 0.0759 13 E 0.0048 0.9465 0.0487 14 L 0.0049 0.9517 0.0434 15 K 0.0048 0.9560 0.0392 16 E 0.0054 0.9527 0.0418 17 T 0.0057 0.9434 0.0509 18 L 0.0098 0.9259 0.0643 19 R 0.0079 0.8847 0.1075 20 K 0.0117 0.6952 0.2931 21 F 0.0678 0.4819 0.4503 22 R 0.1299 0.3577 0.5124 23 F 0.2189 0.2670 0.5141 24 R 0.1580 0.2552 0.5868 25 K 0.0818 0.2782 0.6400 26 E 0.0698 0.1523 0.7779 27 T 0.0988 0.1094 0.7918 28 N 0.2279 0.0517 0.7204 29 N 0.3936 0.0154 0.5910 30 A 0.6053 0.0129 0.3818 31 A 0.9004 0.0035 0.0961 32 I 0.9218 0.0033 0.0749 33 I 0.9256 0.0032 0.0712 34 M 0.9133 0.0043 0.0823 35 K 0.8901 0.0040 0.1059 36 V 0.8048 0.0065 0.1887 37 D 0.4675 0.0126 0.5199 38 K 0.0463 0.1436 0.8101 39 D 0.0328 0.1262 0.8409 40 R 0.1732 0.0821 0.7446 41 Q 0.4909 0.0265 0.4826 42 M 0.8479 0.0060 0.1461 43 V 0.9027 0.0042 0.0931 44 V 0.8930 0.0059 0.1011 45 L 0.8712 0.0068 0.1220 46 E 0.7457 0.0203 0.2340 47 D 0.5707 0.0257 0.4036 48 E 0.2880 0.0465 0.6655 49 L 0.1671 0.0478 0.7851 50 Q 0.1049 0.0682 0.8268 51 N 0.0993 0.0593 0.8414 52 I 0.1264 0.0553 0.8183 53 S 0.1318 0.0343 0.8339 54 P 0.0088 0.8539 0.1373 55 E 0.0069 0.8897 0.1033 56 E 0.0062 0.9089 0.0849 57 L 0.0084 0.9014 0.0902 58 K 0.0092 0.8744 0.1164 59 L 0.0094 0.7708 0.2199 60 E 0.0208 0.5624 0.4167 61 L 0.0922 0.0627 0.8451 62 P 0.0550 0.0512 0.8938 63 E 0.0194 0.1584 0.8222 64 R 0.0219 0.1271 0.8510 65 Q 0.1217 0.0368 0.8415 66 P 0.3211 0.0098 0.6691 67 R 0.7480 0.0249 0.2271 68 F 0.9085 0.0034 0.0881 69 V 0.9192 0.0034 0.0774 70 V 0.9237 0.0033 0.0729 71 Y 0.8967 0.0050 0.0983 72 S 0.8085 0.0086 0.1829 73 Y 0.5581 0.0190 0.4229 74 K 0.3808 0.0450 0.5743 75 Y 0.4399 0.0343 0.5258 76 V 0.5634 0.0283 0.4083 77 H 0.3339 0.0362 0.6299 78 D 0.0644 0.1587 0.7769 79 D 0.0456 0.1160 0.8384 80 G 0.0632 0.1174 0.8194 81 R 0.1759 0.0911 0.7329 82 V 0.3300 0.1026 0.5674 83 S 0.2689 0.0847 0.6463 84 Y 0.1798 0.0228 0.7974 85 P 0.2353 0.0232 0.7416 86 L 0.8339 0.0046 0.1615 87 C 0.9236 0.0034 0.0731 88 F 0.9288 0.0033 0.0679 89 I 0.9172 0.0037 0.0791 90 F 0.8538 0.0081 0.1381 91 S 0.6041 0.0158 0.3801 92 S 0.2392 0.0139 0.7469 93 P 0.0939 0.0820 0.8242 94 V 0.0420 0.0925 0.8655 95 G 0.0566 0.0832 0.8602 96 C 0.0667 0.0513 0.8820 97 K 0.1158 0.0986 0.7856 98 P 0.1019 0.5547 0.3434 99 E 0.0988 0.6954 0.2059 100 Q 0.0952 0.7896 0.1151 101 Q 0.0577 0.8314 0.1109 102 M 0.1113 0.7642 0.1245 103 M 0.0923 0.7613 0.1465 104 Y 0.1152 0.6950 0.1898 105 A 0.0845 0.6586 0.2569 106 G 0.0641 0.5731 0.3628 107 S 0.0526 0.5299 0.4176 108 K 0.0076 0.9019 0.0905 109 N 0.0054 0.9411 0.0535 110 R 0.0048 0.9452 0.0500 111 L 0.0050 0.9465 0.0485 112 V 0.0051 0.9388 0.0561 113 Q 0.0065 0.8724 0.1212 114 T 0.0097 0.7456 0.2447 115 A 0.0609 0.2574 0.6817 116 E 0.0556 0.0345 0.9099 117 L 0.1568 0.0224 0.8208 118 T 0.3623 0.0207 0.6169 119 K 0.7151 0.0098 0.2751 120 V 0.8629 0.0043 0.1327 121 F 0.8734 0.0044 0.1222 122 E 0.8528 0.0051 0.1421 123 I 0.6134 0.0115 0.3751 124 R 0.1376 0.0285 0.8339 125 T 0.0774 0.0147 0.9079 126 T 0.0150 0.6021 0.3829 127 D 0.0185 0.6281 0.3534 128 D 0.0263 0.7103 0.2634 129 L 0.0844 0.3503 0.5653 130 T 0.0805 0.3035 0.6159 131 E 0.0090 0.8944 0.0966 132 T 0.0088 0.9207 0.0705 133 W 0.0066 0.9328 0.0606 134 L 0.0078 0.9322 0.0600 135 K 0.0086 0.9209 0.0706 136 E 0.0074 0.8952 0.0974 137 K 0.0109 0.8419 0.1472 138 L 0.0586 0.6384 0.3030 139 A 0.0773 0.4015 0.5212 140 F 0.1391 0.3127 0.5482 141 F 0.1858 0.1568 0.6575 142 R 0.0494 0.0550 0.8957