# This file is the result of combining several RDB files, specifically # T0141.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0141.t2k.stride-ebghtl.rdb (weight 1.24869) # T0141.t2k.str.rdb (weight 1.53983) # T0141.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 T0141.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0141 # 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 T0141.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 58 # # ============================================ # Comments from T0141.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0141 # 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 T0141.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 58 # # ============================================ # Comments from T0141.t2k.str.rdb # ============================================ # TARGET T0141 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0141.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 58 # # ============================================ # Comments from T0141.t2k.alpha.rdb # ============================================ # TARGET T0141 # 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 T0141.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 58 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0744 0.0244 0.9012 2 L 0.2189 0.0529 0.7281 3 L 0.2039 0.0973 0.6987 4 D 0.1289 0.1430 0.7281 5 E 0.0966 0.1691 0.7342 6 G 0.1087 0.1460 0.7453 7 W 0.2507 0.1444 0.6050 8 L 0.3481 0.1726 0.4792 9 A 0.2355 0.2616 0.5029 10 E 0.1773 0.2166 0.6062 11 A 0.1809 0.2330 0.5861 12 R 0.2362 0.1342 0.6295 13 R 0.3552 0.0759 0.5689 14 V 0.2370 0.0334 0.7296 15 P 0.1588 0.0417 0.7995 16 S 0.1171 0.0439 0.8390 17 P 0.0508 0.1573 0.7919 18 H 0.0606 0.1523 0.7871 19 Y 0.0900 0.2091 0.7009 20 D 0.0987 0.1444 0.7569 21 C 0.1286 0.1088 0.7626 22 R 0.1027 0.0720 0.8253 23 P 0.0679 0.1402 0.7920 24 D 0.0478 0.1847 0.7675 25 D 0.0630 0.1731 0.7639 26 E 0.1209 0.0909 0.7882 27 N 0.2092 0.0369 0.7539 28 P 0.2533 0.0182 0.7285 29 S 0.4630 0.0417 0.4953 30 L 0.9137 0.0044 0.0819 31 L 0.9277 0.0038 0.0684 32 V 0.9303 0.0036 0.0661 33 V 0.9060 0.0052 0.0888 34 H 0.7731 0.0162 0.2107 35 N 0.3626 0.0384 0.5989 36 I 0.1971 0.0785 0.7245 37 S 0.0938 0.0873 0.8190 38 L 0.0758 0.0711 0.8532 39 P 0.0630 0.1093 0.8278 40 P 0.0247 0.5601 0.4152 41 G 0.0141 0.7233 0.2626 42 E 0.0141 0.7524 0.2335 43 F 0.0179 0.7534 0.2286 44 G 0.0231 0.7116 0.2653 45 G 0.0271 0.7110 0.2619 46 P 0.0228 0.7577 0.2195 47 W 0.0211 0.7980 0.1808 48 I 0.0169 0.8543 0.1288 49 D 0.0179 0.8602 0.1220 50 A 0.0213 0.8428 0.1359 51 L 0.0226 0.7919 0.1855 52 F 0.0639 0.6227 0.3135 53 T 0.0474 0.4296 0.5230 54 G 0.0417 0.2431 0.7152 55 T 0.0944 0.1310 0.7746 56 I 0.2028 0.0593 0.7378 57 D 0.1043 0.0424 0.8533 58 P 0.0173 0.2267 0.7560 59 N 0.0178 0.2011 0.7811 60 A 0.0564 0.2471 0.6965 61 H 0.1001 0.1702 0.7297 62 P 0.0960 0.3687 0.5352 63 Y 0.1215 0.3977 0.4808 64 F 0.1904 0.4221 0.3876 65 A 0.2287 0.3450 0.4262 66 G 0.2089 0.2681 0.5231 67 I 0.1383 0.1345 0.7272 68 A 0.0720 0.1615 0.7665 69 H 0.0874 0.1063 0.8063 70 L 0.1783 0.0673 0.7544 71 R 0.3994 0.0301 0.5705 72 V 0.7029 0.0097 0.2874 73 S 0.8004 0.0081 0.1914 74 A 0.8690 0.0062 0.1249 75 H 0.9003 0.0047 0.0950 76 C 0.9114 0.0043 0.0843 77 L 0.9194 0.0038 0.0768 78 I 0.9044 0.0051 0.0905 79 R 0.5842 0.0167 0.3991 80 R 0.0844 0.0612 0.8544 81 D 0.0493 0.0225 0.9282 82 G 0.0998 0.0333 0.8669 83 E 0.6855 0.0083 0.3062 84 I 0.9059 0.0035 0.0906 85 V 0.8837 0.0130 0.1033 86 Q 0.8952 0.0062 0.0987 87 Y 0.8565 0.0063 0.1372 88 V 0.7288 0.0070 0.2642 89 P 0.3847 0.0124 0.6029 90 F 0.0599 0.5385 0.4016 91 D 0.0301 0.5693 0.4006 92 K 0.0567 0.6237 0.3196 93 R 0.1822 0.4797 0.3381 94 A 0.2736 0.4062 0.3202 95 W 0.3447 0.3663 0.2890 96 H 0.3195 0.3222 0.3584 97 A 0.2326 0.2481 0.5193 98 G 0.2186 0.1178 0.6636 99 V 0.1910 0.1178 0.6911 100 S 0.1975 0.1455 0.6570 101 S 0.1795 0.1931 0.6274 102 Y 0.1794 0.1769 0.6437 103 Q 0.1135 0.1374 0.7491 104 G 0.0962 0.0961 0.8077 105 R 0.1148 0.1391 0.7461 106 E 0.1325 0.1786 0.6888 107 R 0.1879 0.1407 0.6714 108 C 0.2458 0.1003 0.6539 109 N 0.2788 0.0643 0.6569 110 D 0.1848 0.1244 0.6908 111 F 0.3229 0.0706 0.6066 112 S 0.5844 0.0276 0.3881 113 I 0.7326 0.0132 0.2542 114 G 0.8223 0.0093 0.1683 115 I 0.8756 0.0065 0.1179 116 E 0.8843 0.0057 0.1099 117 L 0.8224 0.0091 0.1684 118 E 0.6403 0.0337 0.3260 119 G 0.2787 0.0285 0.6928 120 T 0.0884 0.0631 0.8484 121 D 0.0527 0.0721 0.8752 122 T 0.0626 0.0899 0.8475 123 L 0.0528 0.0958 0.8514 124 A 0.0817 0.0585 0.8598 125 Y 0.0811 0.0463 0.8726 126 T 0.0512 0.0875 0.8613 127 D 0.0049 0.9420 0.0531 128 A 0.0045 0.9523 0.0433 129 Q 0.0044 0.9564 0.0391 130 Y 0.0044 0.9597 0.0359 131 Q 0.0044 0.9570 0.0385 132 Q 0.0044 0.9512 0.0443 133 L 0.0044 0.9553 0.0402 134 A 0.0044 0.9589 0.0367 135 A 0.0044 0.9595 0.0361 136 V 0.0044 0.9600 0.0356 137 T 0.0044 0.9601 0.0355 138 N 0.0044 0.9589 0.0368 139 A 0.0044 0.9576 0.0380 140 L 0.0045 0.9527 0.0428 141 I 0.0048 0.9290 0.0662 142 T 0.0057 0.8474 0.1470 143 R 0.0137 0.6590 0.3273 144 Y 0.0631 0.2403 0.6966 145 P 0.0570 0.0452 0.8978 146 A 0.0893 0.0264 0.8844 147 I 0.0752 0.0265 0.8983 148 A 0.0253 0.7211 0.2536 149 N 0.0218 0.7406 0.2377 150 N 0.0489 0.7219 0.2292 151 M 0.3200 0.2058 0.4742 152 T 0.3177 0.1546 0.5278 153 G 0.2889 0.1674 0.5438 154 H 0.1922 0.2543 0.5535 155 C 0.1478 0.2958 0.5564 156 N 0.1918 0.2194 0.5889 157 I 0.2198 0.1033 0.6769 158 A 0.0964 0.0612 0.8424 159 P 0.0806 0.1389 0.7804 160 E 0.0934 0.1373 0.7693 161 R 0.1714 0.1438 0.6847 162 K 0.2504 0.1212 0.6285 163 T 0.3217 0.0883 0.5900 164 D 0.1690 0.0534 0.7776 165 P 0.0618 0.1181 0.8201 166 G 0.0399 0.1429 0.8172 167 P 0.0317 0.1457 0.8226 168 S 0.0412 0.0987 0.8602 169 F 0.1449 0.0366 0.8185 170 D 0.0960 0.0993 0.8047 171 W 0.0059 0.8929 0.1012 172 A 0.0048 0.9269 0.0683 173 R 0.0048 0.9429 0.0523 174 F 0.0048 0.9450 0.0502 175 R 0.0051 0.9366 0.0583 176 A 0.0059 0.8935 0.1007 177 L 0.0081 0.8220 0.1699 178 V 0.0512 0.5512 0.3976 179 T 0.0485 0.1684 0.7831 180 P 0.0571 0.1158 0.8271 181 S 0.0450 0.1827 0.7723 182 S 0.0584 0.2261 0.7155 183 H 0.0635 0.2254 0.7112 184 K 0.0386 0.3718 0.5896 185 E 0.0588 0.3296 0.6116 186 M 0.0862 0.1822 0.7316 187 T 0.0456 0.0416 0.9128