# This file is the result of combining several RDB files, specifically # T0397.t04.dssp-ebghstl.rdb (weight 1.53986) # T0397.t04.stride-ebghtl.rdb (weight 1.24869) # T0397.t04.str2.rdb (weight 1.54758) # T0397.t04.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 T0397.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.stride-ebghtl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0950 0.0151 0.8899 2 K 0.2010 0.0129 0.7861 3 I 0.2364 0.0092 0.7544 4 P 0.2434 0.0102 0.7464 5 K 0.7559 0.0133 0.2308 6 I 0.8945 0.0050 0.1005 7 Y 0.9170 0.0045 0.0785 8 V 0.9055 0.0043 0.0902 9 E 0.7756 0.0301 0.1943 10 G 0.5484 0.0257 0.4259 11 E 0.6349 0.0220 0.3431 12 L 0.5986 0.0381 0.3633 13 N 0.2833 0.0453 0.6714 14 D 0.1036 0.0753 0.8211 15 G 0.0698 0.0463 0.8839 16 D 0.2124 0.0427 0.7448 17 R 0.7631 0.0072 0.2296 18 V 0.9034 0.0036 0.0930 19 A 0.9226 0.0038 0.0736 20 I 0.9262 0.0036 0.0702 21 E 0.9101 0.0052 0.0846 22 K 0.8231 0.0169 0.1601 23 D 0.2306 0.0315 0.7379 24 G 0.0947 0.0404 0.8649 25 N 0.4373 0.0264 0.5363 26 A 0.8275 0.0055 0.1671 27 I 0.9157 0.0038 0.0805 28 I 0.9233 0.0039 0.0728 29 F 0.9163 0.0042 0.0795 30 L 0.8520 0.0069 0.1411 31 E 0.6391 0.0127 0.3482 32 K 0.2498 0.1032 0.6470 33 D 0.1328 0.0879 0.7794 34 E 0.3327 0.0672 0.6001 35 E 0.5856 0.0512 0.3632 36 Y 0.5680 0.0438 0.3882 37 S 0.2111 0.0915 0.6974 38 G 0.0702 0.0695 0.8603 39 N 0.0796 0.0647 0.8557 40 G 0.1038 0.0849 0.8113 41 K 0.3267 0.1346 0.5387 42 L 0.5779 0.2017 0.2204 43 L 0.4598 0.3879 0.1523 44 Y 0.4077 0.4775 0.1147 45 Q 0.3380 0.5654 0.0967 46 V 0.3758 0.5140 0.1102 47 I 0.2249 0.6231 0.1520 48 Y 0.0493 0.8652 0.0855 49 D 0.0140 0.9113 0.0747 50 D 0.0074 0.9224 0.0702 51 L 0.0058 0.9285 0.0657 52 A 0.0064 0.9167 0.0769 53 K 0.0069 0.8598 0.1333 54 Y 0.0177 0.7316 0.2507 55 M 0.0812 0.4181 0.5007 56 S 0.0752 0.1523 0.7725 57 L 0.0214 0.5402 0.4383 58 D 0.0244 0.5248 0.4508 59 T 0.0665 0.4873 0.4462 60 L 0.2946 0.1526 0.5527 61 K 0.4109 0.0663 0.5229 62 K 0.5002 0.0625 0.4373 63 D 0.5870 0.0308 0.3822 64 V 0.8890 0.0047 0.1063 65 L 0.9280 0.0034 0.0686 66 I 0.9280 0.0033 0.0687 67 Q 0.8826 0.0047 0.1126 68 Y 0.4985 0.0072 0.4943 69 P 0.1574 0.0494 0.7932 70 D 0.0832 0.0355 0.8813 71 K 0.0685 0.0792 0.8523 72 H 0.2298 0.0663 0.7039 73 T 0.5924 0.0443 0.3634 74 L 0.7882 0.0164 0.1954 75 T 0.8541 0.0138 0.1321 76 Y 0.8882 0.0125 0.0993 77 L 0.8046 0.0170 0.1784 78 K 0.5379 0.0309 0.4312 79 A 0.0888 0.0673 0.8439 80 G 0.0577 0.0352 0.9072 81 T 0.3718 0.0148 0.6134 82 K 0.8453 0.0049 0.1498 83 L 0.9034 0.0037 0.0930 84 I 0.9164 0.0039 0.0797 85 S 0.9164 0.0035 0.0800 86 V 0.8495 0.0059 0.1446 87 P 0.7420 0.0060 0.2521 88 A 0.4474 0.0526 0.5000 89 E 0.2153 0.0796 0.7052 90 G 0.1909 0.0470 0.7621 91 Y 0.6186 0.0105 0.3709 92 K 0.8581 0.0050 0.1369 93 V 0.8687 0.0048 0.1265 94 Y 0.7802 0.0094 0.2104 95 P 0.7449 0.0122 0.2428 96 I 0.6702 0.0313 0.2986 97 M 0.5432 0.0659 0.3909 98 D 0.3760 0.0777 0.5463 99 F 0.1993 0.1475 0.6532 100 G 0.1673 0.1011 0.7316 101 F 0.3757 0.1127 0.5117 102 R 0.7197 0.0885 0.1918 103 V 0.7110 0.1031 0.1859 104 L 0.5435 0.1224 0.3341 105 K 0.1683 0.1089 0.7227 106 G 0.0574 0.0436 0.8990 107 Y 0.3670 0.0226 0.6104 108 R 0.7962 0.0132 0.1906 109 L 0.8875 0.0107 0.1017 110 A 0.8987 0.0121 0.0892 111 T 0.9076 0.0116 0.0809 112 L 0.8986 0.0106 0.0907 113 E 0.8501 0.0113 0.1386 114 S 0.5715 0.0200 0.4085 115 K 0.2451 0.0741 0.6808 116 K 0.1718 0.0343 0.7939 117 G 0.3372 0.0273 0.6355 118 D 0.6242 0.0139 0.3619 119 L 0.8778 0.0052 0.1169 120 R 0.8990 0.0076 0.0934 121 Y 0.9132 0.0042 0.0826 122 V 0.8488 0.0096 0.1416 123 N 0.6676 0.0133 0.3191 124 S 0.3464 0.0144 0.6392 125 P 0.2829 0.0322 0.6848 126 V 0.3302 0.0417 0.6281 127 S 0.2550 0.0379 0.7070 128 G 0.4875 0.0169 0.4956 129 T 0.8170 0.0055 0.1774 130 V 0.9285 0.0031 0.0684 131 I 0.9260 0.0039 0.0701 132 F 0.9248 0.0034 0.0717 133 M 0.8478 0.0083 0.1439 134 N 0.5747 0.0233 0.4019 135 E 0.3160 0.0208 0.6632 136 I 0.1449 0.0268 0.8283 137 P 0.0932 0.0872 0.8196 138 S 0.0437 0.1812 0.7751 139 E 0.0601 0.1585 0.7814 140 R 0.0897 0.0976 0.8127 141 A 0.1051 0.1077 0.7872 142 N 0.2084 0.0676 0.7240 143 Y 0.8064 0.0073 0.1862 144 V 0.9104 0.0034 0.0862 145 F 0.9308 0.0034 0.0658 146 Y 0.9267 0.0035 0.0698 147 M 0.9003 0.0039 0.0958 148 L 0.6624 0.0091 0.3285 149 E 0.3436 0.0188 0.6376 150 E 0.1121 0.0949 0.7930