# This file is the result of combining several RDB files, specifically # T0319.t06.dssp-ebghstl.rdb (weight 1.53986) # T0319.t06.stride-ebghtl.rdb (weight 1.24869) # T0319.t06.str2.rdb (weight 1.54758) # T0319.t06.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 T0319.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0319 # Using neural net t06-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 T0319.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 21.0135 # # ============================================ # Comments from T0319.t06.stride-ebghtl.rdb # ============================================ # TARGET T0319 # Using neural net t06-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 T0319.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 21.0135 # # ============================================ # Comments from T0319.t06.str2.rdb # ============================================ # TARGET T0319 # Using neural net 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 T0319.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 21.0135 # # ============================================ # Comments from T0319.t06.alpha.rdb # ============================================ # TARGET T0319 # Using neural net 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 T0319.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 21.0135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0910 0.0805 0.8285 2 K 0.3389 0.1890 0.4722 3 F 0.4388 0.3377 0.2235 4 L 0.3776 0.4402 0.1822 5 T 0.3080 0.5075 0.1844 6 T 0.1922 0.6038 0.2040 7 N 0.1782 0.5872 0.2346 8 F 0.1563 0.6063 0.2374 9 L 0.1718 0.5572 0.2710 10 K 0.1847 0.4593 0.3560 11 C 0.1713 0.3004 0.5283 12 S 0.1330 0.2597 0.6072 13 V 0.1459 0.3479 0.5062 14 K 0.1852 0.3488 0.4661 15 A 0.2283 0.2553 0.5165 16 C 0.2794 0.1486 0.5720 17 D 0.2817 0.1178 0.6005 18 T 0.2417 0.1049 0.6534 19 S 0.2042 0.0835 0.7123 20 N 0.1031 0.0954 0.8016 21 D 0.0803 0.0758 0.8439 22 N 0.1284 0.0493 0.8224 23 F 0.2881 0.0216 0.6903 24 P 0.4313 0.0193 0.5494 25 L 0.6810 0.0163 0.3026 26 Q 0.8324 0.0102 0.1574 27 Y 0.8279 0.0102 0.1620 28 D 0.7228 0.0147 0.2626 29 G 0.5328 0.0736 0.3936 30 S 0.4588 0.1201 0.4210 31 K 0.6021 0.1115 0.2864 32 C 0.7154 0.0708 0.2138 33 Q 0.7803 0.0578 0.1619 34 L 0.7944 0.0673 0.1383 35 V 0.6704 0.1001 0.2295 36 Q 0.5772 0.1171 0.3057 37 D 0.3119 0.1759 0.5121 38 E 0.1825 0.1654 0.6521 39 S 0.1954 0.1586 0.6460 40 I 0.3107 0.1355 0.5538 41 E 0.2825 0.1108 0.6067 42 F 0.1648 0.0629 0.7723 43 N 0.1038 0.0141 0.8821 44 P 0.0053 0.9054 0.0893 45 E 0.0049 0.9359 0.0592 46 F 0.0050 0.9448 0.0501 47 L 0.0065 0.9435 0.0500 48 L 0.0091 0.9180 0.0729 49 N 0.0088 0.8347 0.1565 50 I 0.0155 0.7578 0.2267 51 V 0.0484 0.5457 0.4059 52 D 0.0356 0.4904 0.4739 53 R 0.0366 0.5307 0.4327 54 V 0.1161 0.2446 0.6393 55 D 0.0905 0.1735 0.7360 56 W 0.0063 0.9360 0.0578 57 P 0.0047 0.9571 0.0382 58 A 0.0047 0.9587 0.0365 59 V 0.0047 0.9603 0.0350 60 L 0.0047 0.9605 0.0348 61 T 0.0047 0.9596 0.0357 62 V 0.0047 0.9585 0.0368 63 A 0.0047 0.9560 0.0393 64 A 0.0049 0.9451 0.0501 65 E 0.0058 0.8795 0.1147 66 L 0.0462 0.4652 0.4886 67 G 0.0401 0.1035 0.8564 68 N 0.0564 0.2484 0.6952 69 N 0.0403 0.3467 0.6130 70 A 0.0608 0.2771 0.6621 71 L 0.0926 0.0312 0.8762 72 P 0.0690 0.0264 0.9046 73 P 0.0417 0.1822 0.7761 74 T 0.0651 0.1561 0.7788 75 K 0.0841 0.0491 0.8669 76 P 0.0720 0.0500 0.8780 77 S 0.0886 0.0584 0.8530 78 F 0.0840 0.0346 0.8814 79 P 0.0669 0.0966 0.8365 80 S 0.0511 0.2996 0.6493 81 S 0.0917 0.3286 0.5797 82 I 0.0892 0.5937 0.3171 83 Q 0.1025 0.5539 0.3436 84 E 0.1166 0.4836 0.3998 85 L 0.0812 0.4296 0.4891 86 T 0.0710 0.3010 0.6280 87 D 0.0390 0.3816 0.5794 88 D 0.0214 0.3961 0.5825 89 D 0.0344 0.4865 0.4790 90 M 0.0063 0.9207 0.0730 91 A 0.0049 0.9494 0.0457 92 I 0.0048 0.9520 0.0432 93 L 0.0047 0.9553 0.0400 94 N 0.0047 0.9571 0.0382 95 D 0.0047 0.9576 0.0377 96 L 0.0047 0.9579 0.0375 97 H 0.0049 0.9579 0.0372 98 T 0.0052 0.9556 0.0392 99 L 0.0056 0.9464 0.0481 100 L 0.0072 0.9153 0.0775 101 L 0.0155 0.8063 0.1782 102 Q 0.0322 0.6778 0.2900 103 T 0.1104 0.4922 0.3974 104 S 0.3299 0.3251 0.3450 105 I 0.5721 0.2129 0.2149 106 A 0.6761 0.1172 0.2066 107 E 0.5795 0.0623 0.3581 108 G 0.4984 0.0268 0.4748 109 E 0.7608 0.0129 0.2263 110 M 0.8779 0.0047 0.1175 111 K 0.8497 0.0055 0.1448 112 C 0.6141 0.0094 0.3765 113 R 0.0224 0.1404 0.8372 114 N 0.0215 0.0957 0.8828 115 C 0.0942 0.0786 0.8272 116 G 0.1055 0.0351 0.8593 117 H 0.4779 0.0172 0.5049 118 I 0.8338 0.0100 0.1562 119 Y 0.8384 0.0114 0.1502 120 Y 0.7875 0.0130 0.1995 121 I 0.5656 0.0543 0.3801 122 K 0.3462 0.1172 0.5366 123 N 0.1089 0.0890 0.8021 124 G 0.1047 0.0683 0.8270 125 I 0.1919 0.0625 0.7456 126 P 0.1801 0.2019 0.6180 127 N 0.1213 0.3234 0.5553 128 L 0.1682 0.2807 0.5511 129 L 0.1893 0.1202 0.6905 130 L 0.1035 0.0490 0.8476 131 P 0.0663 0.0434 0.8903 132 P 0.0204 0.5069 0.4727 133 H 0.0274 0.4381 0.5344 134 L 0.0739 0.3076 0.6185 135 V 0.0520 0.0442 0.9038