# This file is the result of combining several RDB files, specifically # T0331.t04.dssp-ebghstl.rdb (weight 1.53986) # T0331.t04.stride-ebghtl.rdb (weight 1.24869) # T0331.t04.str2.rdb (weight 1.54758) # T0331.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 T0331.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0331 # 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 T0331.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 2 # # ============================================ # Comments from T0331.t04.stride-ebghtl.rdb # ============================================ # TARGET T0331 # 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 T0331.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 2 # # ============================================ # Comments from T0331.t04.str2.rdb # ============================================ # TARGET T0331 # 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 T0331.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 2 # # ============================================ # Comments from T0331.t04.alpha.rdb # ============================================ # TARGET T0331 # 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 T0331.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0718 0.0595 0.8687 2 E 0.0993 0.1274 0.7733 3 L 0.0435 0.6194 0.3371 4 K 0.0276 0.6903 0.2821 5 D 0.0389 0.7003 0.2609 6 I 0.0100 0.9159 0.0741 7 M 0.0071 0.9361 0.0568 8 H 0.0091 0.9318 0.0592 9 I 0.0123 0.9037 0.0841 10 L 0.0203 0.8283 0.1514 11 E 0.0186 0.6588 0.3226 12 D 0.0291 0.4096 0.5614 13 M 0.1425 0.1607 0.6968 14 K 0.2814 0.0764 0.6422 15 V 0.6937 0.0322 0.2741 16 G 0.7684 0.0228 0.2087 17 V 0.8705 0.0137 0.1158 18 F 0.8665 0.0156 0.1179 19 A 0.8186 0.0159 0.1655 20 T 0.7293 0.0212 0.2495 21 L 0.4858 0.1013 0.4128 22 D 0.1931 0.1537 0.6532 23 E 0.0571 0.2161 0.7268 24 Y 0.0743 0.1133 0.8124 25 G 0.0647 0.0544 0.8809 26 N 0.0945 0.0335 0.8721 27 P 0.0757 0.2572 0.6671 28 H 0.1189 0.3221 0.5589 29 A 0.2145 0.3066 0.4789 30 R 0.3079 0.2543 0.4378 31 H 0.3283 0.2863 0.3854 32 A 0.3558 0.2182 0.4260 33 H 0.4729 0.1603 0.3668 34 I 0.6683 0.0939 0.2378 35 T 0.7082 0.0963 0.1955 36 A 0.7167 0.0923 0.1910 37 A 0.5630 0.1256 0.3114 38 N 0.3833 0.1059 0.5108 39 E 0.2636 0.1793 0.5572 40 E 0.2751 0.0898 0.6351 41 G 0.4433 0.0475 0.5092 42 I 0.8066 0.0119 0.1815 43 F 0.8918 0.0093 0.0989 44 F 0.8943 0.0098 0.0958 45 M 0.8203 0.0146 0.1650 46 T 0.5149 0.0209 0.4642 47 S 0.1131 0.0266 0.8603 48 P 0.0324 0.1338 0.8338 49 E 0.0379 0.1878 0.7744 50 T 0.0631 0.3278 0.6092 51 H 0.0648 0.5246 0.4106 52 F 0.0378 0.7795 0.1827 53 Y 0.0184 0.8877 0.0939 54 D 0.0129 0.9097 0.0774 55 Q 0.0132 0.8956 0.0911 56 L 0.0238 0.8104 0.1658 57 M 0.0311 0.5237 0.4452 58 G 0.0280 0.2202 0.7518 59 D 0.0803 0.0799 0.8398 60 Q 0.0696 0.2312 0.6992 61 R 0.3591 0.2391 0.4018 62 V 0.7547 0.0984 0.1470 63 A 0.8210 0.0666 0.1123 64 M 0.8482 0.0510 0.1008 65 T 0.7924 0.0626 0.1450 66 A 0.7568 0.0477 0.1955 67 I 0.5892 0.0657 0.3452 68 S 0.3067 0.0863 0.6070 69 E 0.1165 0.2792 0.6043 70 E 0.0725 0.1444 0.7831 71 G 0.1184 0.0687 0.8129 72 Y 0.5405 0.0321 0.4275 73 L 0.8311 0.0088 0.1601 74 I 0.8440 0.0150 0.1410 75 Q 0.8734 0.0122 0.1144 76 V 0.9050 0.0081 0.0869 77 V 0.9030 0.0065 0.0905 78 R 0.8913 0.0072 0.1015 79 V 0.8150 0.0206 0.1643 80 E 0.5586 0.0415 0.3999 81 G 0.3266 0.0335 0.6400 82 T 0.3825 0.0359 0.5817 83 A 0.4129 0.0400 0.5471 84 R 0.3813 0.0524 0.5664 85 P 0.3465 0.1438 0.5097 86 V 0.2279 0.2919 0.4802 87 E 0.1546 0.4043 0.4411 88 N 0.0621 0.5979 0.3400 89 D 0.0218 0.8123 0.1659 90 Y 0.0186 0.8792 0.1023 91 L 0.0119 0.9266 0.0615 92 K 0.0095 0.9354 0.0552 93 T 0.0086 0.9328 0.0586 94 V 0.0084 0.9150 0.0766 95 F 0.0176 0.8518 0.1305 96 A 0.0167 0.7592 0.2240 97 D 0.0236 0.5945 0.3819 98 N 0.0857 0.1222 0.7921 99 P 0.0135 0.4867 0.4998 100 Y 0.0357 0.5322 0.4321 101 Y 0.0620 0.6490 0.2890 102 Q 0.0682 0.6838 0.2480 103 H 0.1088 0.6037 0.2875 104 I 0.1452 0.5149 0.3399 105 Y 0.1551 0.3097 0.5352 106 K 0.0853 0.3221 0.5926 107 D 0.0562 0.2957 0.6481 108 E 0.0473 0.2716 0.6811 109 S 0.0742 0.2081 0.7177 110 S 0.0414 0.2983 0.6603 111 D 0.1038 0.2561 0.6402 112 T 0.3918 0.2366 0.3716 113 M 0.5996 0.1262 0.2742 114 Q 0.7336 0.0747 0.1918 115 V 0.8512 0.0506 0.0982 116 F 0.8504 0.0539 0.0957 117 Q 0.8659 0.0412 0.0929 118 I 0.7892 0.0754 0.1354 119 Y 0.6231 0.0804 0.2965 120 A 0.2862 0.1061 0.6077 121 G 0.1456 0.0695 0.7849 122 H 0.1874 0.0804 0.7323 123 G 0.2244 0.0886 0.6870 124 F 0.3546 0.1304 0.5150 125 Y 0.4489 0.1619 0.3892 126 H 0.4297 0.1454 0.4248 127 S 0.3835 0.1106 0.5059 128 L 0.2280 0.1060 0.6659 129 T 0.1467 0.0717 0.7816 130 Q 0.0596 0.1389 0.8015 131 G 0.0615 0.0969 0.8416 132 H 0.2184 0.0739 0.7077 133 K 0.4565 0.0581 0.4854 134 Y 0.6844 0.0420 0.2735 135 I 0.8021 0.0373 0.1606 136 F 0.7936 0.0404 0.1660 137 S 0.7103 0.0408 0.2489 138 I 0.4526 0.0802 0.4672 139 G 0.2275 0.0606 0.7119 140 Q 0.1489 0.0912 0.7599 141 G 0.1844 0.1069 0.7087 142 E 0.2695 0.1591 0.5714 143 H 0.2136 0.3469 0.4395 144 S 0.2030 0.3522 0.4448 145 E 0.2149 0.3809 0.4042 146 V 0.2477 0.2955 0.4568 147 R 0.1894 0.2775 0.5331 148 A 0.1543 0.2203 0.6254 149 L 0.0745 0.0946 0.8309