# This file is the result of combining several RDB files, specifically # T0276.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0276.t2k.stride-ebghtl.rdb (weight 1.24869) # T0276.t2k.str2.rdb (weight 1.54758) # T0276.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 T0276.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0276 # 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 T0276.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 195 # # ============================================ # Comments from T0276.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0276 # 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 T0276.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 195 # # ============================================ # Comments from T0276.t2k.str2.rdb # ============================================ # TARGET T0276 # 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 T0276.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 195 # # ============================================ # Comments from T0276.t2k.alpha.rdb # ============================================ # TARGET T0276 # 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 T0276.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 195 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0489 0.0787 0.8724 2 T 0.0573 0.1554 0.7873 3 K 0.0060 0.8811 0.1129 4 A 0.0050 0.9329 0.0621 5 E 0.0049 0.9457 0.0494 6 L 0.0047 0.9505 0.0447 7 R 0.0047 0.9562 0.0391 8 R 0.0047 0.9561 0.0391 9 R 0.0047 0.9561 0.0392 10 A 0.0047 0.9567 0.0386 11 R 0.0047 0.9549 0.0404 12 A 0.0048 0.9471 0.0481 13 A 0.0049 0.9317 0.0634 14 W 0.0058 0.8975 0.0966 15 R 0.0069 0.7770 0.2161 16 R 0.0120 0.5619 0.4260 17 L 0.0375 0.2601 0.7024 18 D 0.0418 0.2360 0.7223 19 L 0.0174 0.4384 0.5442 20 K 0.0241 0.5176 0.4583 21 A 0.0196 0.6111 0.3692 22 L 0.0129 0.7407 0.2464 23 S 0.0094 0.8416 0.1490 24 R 0.0053 0.9280 0.0666 25 A 0.0055 0.9402 0.0544 26 V 0.0050 0.9481 0.0470 27 G 0.0049 0.9499 0.0452 28 A 0.0054 0.9418 0.0528 29 A 0.0058 0.9243 0.0699 30 L 0.0064 0.8883 0.1052 31 L 0.0099 0.7575 0.2326 32 P 0.0145 0.5431 0.4423 33 W 0.0459 0.3404 0.6138 34 L 0.0206 0.5658 0.4136 35 R 0.0256 0.5963 0.3781 36 E 0.0505 0.5669 0.3826 37 R 0.0694 0.4091 0.5215 38 G 0.1007 0.1874 0.7118 39 F 0.1730 0.0614 0.7656 40 R 0.2667 0.0699 0.6635 41 H 0.8070 0.0101 0.1829 42 I 0.8958 0.0060 0.0982 43 L 0.9138 0.0050 0.0812 44 L 0.9018 0.0062 0.0920 45 Y 0.8088 0.0118 0.1794 46 H 0.5083 0.0129 0.4788 47 P 0.2204 0.0229 0.7567 48 L 0.0728 0.0800 0.8472 49 P 0.0383 0.1393 0.8224 50 H 0.0354 0.1474 0.8173 51 E 0.0844 0.1594 0.7562 52 L 0.1029 0.1740 0.7231 53 N 0.1654 0.1490 0.6857 54 L 0.0156 0.7956 0.1888 55 L 0.0067 0.9196 0.0738 56 P 0.0056 0.9400 0.0544 57 L 0.0055 0.9420 0.0525 58 M 0.0059 0.9346 0.0595 59 E 0.0061 0.8881 0.1058 60 A 0.0086 0.7799 0.2115 61 Y 0.0504 0.3059 0.6437 62 P 0.0325 0.0405 0.9270 63 A 0.0970 0.0236 0.8795 64 R 0.5202 0.0088 0.4710 65 Y 0.8213 0.0045 0.1742 66 Y 0.8759 0.0049 0.1192 67 L 0.8289 0.0048 0.1663 68 P 0.6590 0.0085 0.3325 69 K 0.4949 0.0115 0.4937 70 V 0.4249 0.0230 0.5521 71 A 0.2259 0.0376 0.7365 72 G 0.0912 0.1170 0.7918 73 K 0.0533 0.1206 0.8261 74 G 0.1455 0.0838 0.7707 75 L 0.5247 0.0216 0.4537 76 T 0.7485 0.0131 0.2384 77 V 0.8335 0.0106 0.1559 78 H 0.7842 0.0129 0.2029 79 P 0.7164 0.0177 0.2658 80 F 0.3770 0.0458 0.5772 81 G 0.2126 0.0539 0.7335 82 P 0.2075 0.0938 0.6987 83 L 0.2106 0.0888 0.7005 84 A 0.2087 0.0930 0.6983 85 P 0.1461 0.1803 0.6736 86 G 0.1126 0.1375 0.7498 87 P 0.0970 0.2283 0.6748 88 F 0.1700 0.1619 0.6682 89 G 0.1529 0.0939 0.7532 90 L 0.2029 0.0547 0.7423 91 L 0.2697 0.0545 0.6757 92 E 0.2476 0.0396 0.7128 93 P 0.1894 0.0457 0.7649 94 T 0.1262 0.0596 0.8142 95 T 0.0766 0.1018 0.8216 96 P 0.0655 0.1002 0.8342 97 P 0.0706 0.1595 0.7699 98 E 0.0738 0.1438 0.7824 99 D 0.0794 0.1475 0.7731 100 P 0.0705 0.2392 0.6903 101 R 0.0977 0.1638 0.7385 102 V 0.2096 0.0881 0.7023 103 L 0.2751 0.0109 0.7140 104 D 0.4186 0.0378 0.5436 105 L 0.9204 0.0040 0.0756 106 V 0.9311 0.0033 0.0656 107 V 0.9260 0.0036 0.0704 108 V 0.8551 0.0061 0.1388 109 P 0.5930 0.0189 0.3881 110 G 0.4581 0.0320 0.5099 111 L 0.7173 0.0343 0.2484 112 A 0.7688 0.0249 0.2063 113 F 0.8058 0.0120 0.1822 114 D 0.2831 0.0150 0.7019 115 R 0.0160 0.1264 0.8576 116 E 0.0444 0.0279 0.9277 117 G 0.0725 0.0362 0.8912 118 Y 0.3256 0.0214 0.6530 119 R 0.7795 0.0112 0.2093 120 L 0.7315 0.0305 0.2380 121 G 0.5982 0.0411 0.3607 122 H 0.4077 0.0571 0.5352 123 G 0.2547 0.0638 0.6815 124 Q 0.2174 0.0972 0.6854 125 G 0.1613 0.2082 0.6305 126 F 0.1332 0.5663 0.3005 127 Y 0.0951 0.7041 0.2008 128 D 0.0570 0.7889 0.1542 129 R 0.0305 0.8513 0.1182 130 F 0.0189 0.8629 0.1182 131 L 0.0198 0.8125 0.1677 132 K 0.0245 0.7085 0.2670 133 E 0.0384 0.4971 0.4646 134 V 0.0739 0.1605 0.7656 135 R 0.0504 0.0609 0.8886 136 A 0.0944 0.0252 0.8804 137 A 0.2245 0.0188 0.7567 138 T 0.7665 0.0076 0.2259 139 V 0.8999 0.0059 0.0943 140 G 0.9096 0.0047 0.0857 141 V 0.9042 0.0050 0.0907 142 V 0.8341 0.0099 0.1559 143 P 0.6178 0.0284 0.3537 144 Q 0.4473 0.0856 0.4670 145 A 0.3901 0.2007 0.4092 146 L 0.4271 0.1998 0.3731 147 L 0.4453 0.1554 0.3992 148 F 0.2532 0.1305 0.6163 149 P 0.1093 0.1855 0.7052 150 A 0.1098 0.1422 0.7480 151 L 0.1614 0.0386 0.8001 152 P 0.1379 0.0194 0.8427 153 R 0.1175 0.0551 0.8275 154 D 0.0892 0.0634 0.8474 155 P 0.0470 0.2595 0.6935 156 W 0.0953 0.1964 0.7082 157 D 0.1977 0.1239 0.6784 158 V 0.3461 0.0413 0.6126 159 P 0.3230 0.0340 0.6431 160 V 0.3408 0.0618 0.5974 161 D 0.3762 0.0901 0.5337 162 H 0.7901 0.0306 0.1794 163 L 0.8842 0.0112 0.1046 164 A 0.8686 0.0083 0.1231 165 T 0.4430 0.0104 0.5466 166 E 0.0642 0.1144 0.8214 167 A 0.0565 0.0872 0.8563 168 G 0.1985 0.1067 0.6948 169 V 0.5795 0.0353 0.3852 170 E 0.7689 0.0307 0.2004 171 A 0.7553 0.0327 0.2120 172 V 0.5363 0.0459 0.4178 173 K 0.3177 0.0438 0.6385 174 R 0.2179 0.0419 0.7402 175 P 0.1810 0.0676 0.7514 176 A 0.1457 0.0456 0.8087 177 P 0.1190 0.0666 0.8144 178 G 0.0920 0.0413 0.8667 179 P 0.0826 0.1038 0.8136 180 G 0.0935 0.0958 0.8107 181 G 0.1999 0.1003 0.6998 182 L 0.3231 0.0759 0.6010 183 L 0.2519 0.0549 0.6932 184 D 0.0576 0.0259 0.9165