# This file is the result of combining several RDB files, specifically # T0257.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0257.t2k.stride-ebghtl.rdb (weight 1.24869) # T0257.t2k.str2.rdb (weight 1.54758) # T0257.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 T0257.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0257 # 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 T0257.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 56 # # ============================================ # Comments from T0257.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0257 # 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 T0257.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 56 # # ============================================ # Comments from T0257.t2k.str2.rdb # ============================================ # TARGET T0257 # 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 T0257.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 56 # # ============================================ # Comments from T0257.t2k.alpha.rdb # ============================================ # TARGET T0257 # 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 T0257.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 56 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1532 0.0474 0.7995 2 A 0.3191 0.0311 0.6497 3 V 0.4757 0.0257 0.4987 4 D 0.6403 0.0271 0.3326 5 M 0.8000 0.0216 0.1784 6 F 0.8873 0.0113 0.1014 7 I 0.8840 0.0089 0.1071 8 K 0.8598 0.0094 0.1309 9 I 0.7374 0.0275 0.2351 10 G 0.2046 0.0554 0.7399 11 D 0.0653 0.0394 0.8953 12 V 0.2697 0.0374 0.6929 13 K 0.2357 0.0652 0.6991 14 G 0.1564 0.0694 0.7742 15 E 0.1998 0.1689 0.6312 16 S 0.2414 0.2203 0.5383 17 K 0.2005 0.3089 0.4906 18 D 0.1249 0.4141 0.4610 19 K 0.0726 0.3700 0.5574 20 T 0.0769 0.2356 0.6874 21 H 0.1357 0.1350 0.7293 22 A 0.0848 0.1893 0.7259 23 E 0.1039 0.1278 0.7683 24 E 0.5696 0.0552 0.3752 25 I 0.8069 0.0212 0.1719 26 D 0.8889 0.0067 0.1044 27 V 0.8896 0.0086 0.1018 28 L 0.8490 0.0202 0.1308 29 A 0.8530 0.0116 0.1355 30 W 0.7738 0.0258 0.2004 31 S 0.6241 0.0387 0.3372 32 W 0.3372 0.1168 0.5460 33 G 0.2837 0.0948 0.6215 34 M 0.3818 0.0901 0.5281 35 S 0.3845 0.0658 0.5498 36 Q 0.4025 0.0453 0.5522 37 S 0.3359 0.0571 0.6071 38 G 0.3418 0.0655 0.5928 39 S 0.2460 0.0488 0.7052 40 M 0.1497 0.1580 0.6923 41 H 0.1438 0.1274 0.7288 42 M 0.1560 0.1073 0.7367 43 G 0.1209 0.0733 0.8059 44 G 0.0918 0.0672 0.8411 45 G 0.0990 0.0569 0.8441 46 G 0.1441 0.0679 0.7880 47 G 0.2107 0.0655 0.7238 48 A 0.2153 0.0726 0.7121 49 G 0.2427 0.0472 0.7102 50 K 0.4101 0.0304 0.5595 51 V 0.6332 0.0188 0.3481 52 N 0.6817 0.0201 0.2982 53 V 0.6360 0.0239 0.3401 54 Q 0.4449 0.0392 0.5159 55 D 0.5691 0.0264 0.4044 56 L 0.8526 0.0064 0.1410 57 S 0.8966 0.0065 0.0969 58 F 0.8792 0.0077 0.1131 59 T 0.7646 0.0237 0.2117 60 K 0.6356 0.0267 0.3377 61 Y 0.4311 0.0632 0.5057 62 I 0.2819 0.0888 0.6294 63 D 0.1404 0.1503 0.7093 64 K 0.0364 0.3123 0.6513 65 S 0.0577 0.3515 0.5908 66 T 0.0478 0.3687 0.5835 67 P 0.0064 0.9026 0.0910 68 N 0.0053 0.9346 0.0601 69 L 0.0048 0.9456 0.0496 70 M 0.0051 0.9484 0.0465 71 M 0.0051 0.9497 0.0451 72 A 0.0057 0.9391 0.0553 73 C 0.0078 0.9105 0.0817 74 S 0.0117 0.7938 0.1945 75 S 0.0374 0.3589 0.6037 76 G 0.0257 0.0598 0.9145 77 K 0.0974 0.0578 0.8448 78 H 0.2722 0.0473 0.6805 79 Y 0.1673 0.0683 0.7645 80 P 0.1851 0.1057 0.7092 81 Q 0.6021 0.0400 0.3580 82 A 0.8525 0.0054 0.1421 83 K 0.9217 0.0033 0.0749 84 L 0.9306 0.0032 0.0662 85 T 0.9291 0.0033 0.0676 86 I 0.9238 0.0031 0.0731 87 R 0.8985 0.0047 0.0969 88 K 0.8528 0.0053 0.1419 89 A 0.5744 0.0241 0.4015 90 G 0.1741 0.0391 0.7868 91 G 0.0521 0.0327 0.9153 92 E 0.0616 0.0333 0.9051 93 N 0.3035 0.0199 0.6766 94 Q 0.6630 0.0082 0.3289 95 V 0.7395 0.0086 0.2518 96 E 0.8181 0.0081 0.1738 97 Y 0.8842 0.0057 0.1101 98 L 0.9174 0.0037 0.0790 99 I 0.9312 0.0032 0.0656 100 I 0.9276 0.0035 0.0690 101 T 0.9229 0.0036 0.0735 102 L 0.8759 0.0081 0.1160 103 K 0.5486 0.0490 0.4025 104 E 0.5113 0.0191 0.4696 105 V 0.8066 0.0044 0.1889 106 L 0.9121 0.0037 0.0841 107 V 0.9204 0.0030 0.0766 108 S 0.8661 0.0168 0.1171 109 S 0.8848 0.0039 0.1113 110 V 0.8143 0.0073 0.1784 111 S 0.6931 0.0080 0.2989 112 T 0.5649 0.0388 0.3964 113 G 0.3385 0.0644 0.5971 114 G 0.1945 0.0585 0.7469 115 S 0.1109 0.0779 0.8113 116 G 0.0761 0.0829 0.8410 117 G 0.0535 0.0926 0.8539 118 E 0.0673 0.0764 0.8563 119 D 0.1403 0.0515 0.8082 120 R 0.3314 0.0187 0.6499 121 L 0.5373 0.0153 0.4474 122 T 0.6871 0.0258 0.2870 123 E 0.7990 0.0148 0.1862 124 N 0.8817 0.0066 0.1117 125 V 0.9079 0.0043 0.0879 126 T 0.9229 0.0037 0.0734 127 L 0.9125 0.0049 0.0826 128 N 0.8927 0.0061 0.1012 129 F 0.8182 0.0154 0.1664 130 A 0.7635 0.0370 0.1995 131 Q 0.8597 0.0092 0.1310 132 V 0.8795 0.0042 0.1163 133 Q 0.8990 0.0045 0.0965 134 V 0.9111 0.0040 0.0849 135 D 0.9048 0.0049 0.0903 136 Y 0.8856 0.0045 0.1099 137 Q 0.7847 0.0063 0.2090 138 P 0.6578 0.0147 0.3275 139 Q 0.3363 0.0460 0.6177 140 K 0.1759 0.0373 0.7869 141 A 0.0976 0.0705 0.8319 142 D 0.0950 0.0590 0.8459 143 G 0.0929 0.0499 0.8571 144 A 0.1338 0.0575 0.8087 145 K 0.1533 0.0872 0.7594 146 D 0.1028 0.0716 0.8256 147 G 0.1281 0.0515 0.8204 148 G 0.2610 0.0499 0.6891 149 P 0.5266 0.0436 0.4298 150 V 0.6662 0.0269 0.3069 151 K 0.7274 0.0369 0.2357 152 Y 0.6967 0.0519 0.2514 153 G 0.6800 0.0488 0.2712 154 W 0.6629 0.0524 0.2847 155 N 0.5462 0.0722 0.3817 156 I 0.1579 0.5018 0.3402 157 R 0.0937 0.5467 0.3596 158 Q 0.0995 0.4575 0.4429 159 N 0.1284 0.2431 0.6285 160 V 0.1989 0.2116 0.5895 161 Q 0.2127 0.1600 0.6273 162 A 0.0484 0.0451 0.9065