# This file is the result of combining several RDB files, specifically # T0216.t04.dssp-ebghstl.rdb (weight 1.53986) # T0216.t04.stride-ebghtl.rdb (weight 1.24869) # T0216.t04.str2.rdb (weight 1.54758) # T0216.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 T0216.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 1 # # ============================================ # Comments from T0216.t04.stride-ebghtl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 1 # # ============================================ # Comments from T0216.t04.str2.rdb # ============================================ # TARGET T0216 # 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 T0216.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 1 # # ============================================ # Comments from T0216.t04.alpha.rdb # ============================================ # TARGET T0216 # 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 T0216.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1295 0.0400 0.8305 2 T 0.1649 0.0733 0.7618 3 F 0.0454 0.7748 0.1799 4 E 0.0172 0.8840 0.0988 5 E 0.0193 0.8952 0.0856 6 F 0.0150 0.8987 0.0863 7 K 0.0105 0.9216 0.0679 8 D 0.0091 0.9260 0.0648 9 R 0.0100 0.9208 0.0692 10 L 0.0134 0.9286 0.0579 11 F 0.0188 0.9221 0.0591 12 A 0.0262 0.9171 0.0567 13 L 0.0368 0.8983 0.0649 14 A 0.0614 0.8420 0.0967 15 K 0.0597 0.7698 0.1704 16 K 0.0582 0.6130 0.3288 17 N 0.0544 0.1821 0.7635 18 G 0.0793 0.0275 0.8932 19 V 0.4982 0.0141 0.4877 20 E 0.8566 0.0073 0.1361 21 V 0.8855 0.0057 0.1088 22 Q 0.8892 0.0064 0.1044 23 I 0.8655 0.0093 0.1252 24 S 0.8123 0.0204 0.1673 25 F 0.7640 0.0467 0.1893 26 L 0.6364 0.0804 0.2832 27 E 0.5545 0.0961 0.3493 28 T 0.4362 0.1307 0.4331 29 R 0.4348 0.1395 0.4256 30 E 0.5511 0.1341 0.3147 31 F 0.6030 0.1216 0.2754 32 S 0.6181 0.1301 0.2518 33 L 0.6763 0.1242 0.1995 34 R 0.6823 0.1265 0.1912 35 L 0.5479 0.1597 0.2924 36 A 0.3010 0.1762 0.5227 37 N 0.1128 0.0842 0.8030 38 G 0.0979 0.0512 0.8508 39 D 0.1733 0.0604 0.7663 40 L 0.1480 0.4013 0.4507 41 D 0.0984 0.4799 0.4218 42 Q 0.1303 0.5019 0.3677 43 Y 0.2160 0.3618 0.4222 44 T 0.1908 0.2994 0.5098 45 D 0.1869 0.2298 0.5833 46 A 0.1120 0.1993 0.6888 47 G 0.1100 0.1032 0.7868 48 K 0.2549 0.1090 0.6360 49 F 0.5311 0.0577 0.4111 50 N 0.6265 0.0334 0.3401 51 V 0.8198 0.0148 0.1654 52 E 0.8845 0.0127 0.1028 53 I 0.9044 0.0090 0.0866 54 K 0.9028 0.0092 0.0880 55 V 0.9020 0.0104 0.0876 56 L 0.7871 0.0275 0.1854 57 K 0.6225 0.0543 0.3232 58 D 0.1980 0.0498 0.7522 59 G 0.1043 0.0452 0.8505 60 K 0.2351 0.0547 0.7102 61 T 0.4047 0.0526 0.5426 62 G 0.3591 0.0532 0.5876 63 T 0.5688 0.0557 0.3755 64 F 0.7112 0.0676 0.2213 65 R 0.6210 0.1387 0.2403 66 T 0.6029 0.1650 0.2321 67 Q 0.6023 0.1896 0.2081 68 V 0.5910 0.2205 0.1885 69 L 0.4748 0.2152 0.3100 70 E 0.2598 0.1998 0.5404 71 N 0.1167 0.0394 0.8439 72 P 0.0137 0.5570 0.4293 73 E 0.0134 0.6412 0.3454 74 K 0.0205 0.7410 0.2386 75 C 0.0308 0.7510 0.2182 76 F 0.0191 0.8317 0.1492 77 E 0.0099 0.9196 0.0705 78 E 0.0102 0.9188 0.0710 79 A 0.0126 0.8934 0.0941 80 L 0.0273 0.8212 0.1516 81 S 0.0243 0.6763 0.2994 82 N 0.0327 0.4367 0.5306 83 L 0.1258 0.1837 0.6905 84 Q 0.2395 0.0904 0.6701 85 V 0.3064 0.0669 0.6266 86 K 0.2033 0.0689 0.7278 87 D 0.1525 0.0567 0.7908 88 S 0.0466 0.3321 0.6213 89 E 0.0633 0.4626 0.4741 90 E 0.1280 0.4516 0.4203 91 K 0.2117 0.4105 0.3778 92 E 0.3486 0.3652 0.2861 93 Y 0.4878 0.3051 0.2071 94 F 0.5851 0.2205 0.1943 95 F 0.5111 0.1881 0.3008 96 E 0.2954 0.1883 0.5163 97 G 0.0945 0.0852 0.8203 98 G 0.0853 0.0918 0.8229 99 K 0.2366 0.1940 0.5694 100 E 0.4212 0.2407 0.3381 101 Y 0.3171 0.4003 0.2826 102 R 0.3069 0.4335 0.2596 103 E 0.3410 0.4416 0.2174 104 M 0.2483 0.5398 0.2119 105 E 0.2707 0.5171 0.2122 106 T 0.2966 0.4869 0.2165 107 Y 0.2898 0.4825 0.2277 108 V 0.2527 0.4437 0.3037 109 G 0.2072 0.2990 0.4937 110 R 0.2375 0.3350 0.4275 111 F 0.2710 0.3817 0.3473 112 E 0.2705 0.3502 0.3793 113 K 0.3838 0.3011 0.3150 114 L 0.3501 0.1774 0.4725 115 S 0.3185 0.1462 0.5353 116 V 0.1996 0.5319 0.2685 117 K 0.1556 0.6182 0.2262 118 E 0.1204 0.6500 0.2296 119 K 0.0802 0.6656 0.2543 120 M 0.0707 0.6569 0.2724 121 D 0.0437 0.7123 0.2440 122 M 0.0152 0.8646 0.1202 123 A 0.0129 0.8758 0.1114 124 K 0.0110 0.8879 0.1011 125 K 0.0133 0.8657 0.1210 126 A 0.0163 0.8210 0.1628 127 H 0.0249 0.7225 0.2526 128 E 0.0232 0.7291 0.2476 129 S 0.0297 0.7052 0.2652 130 A 0.0315 0.6546 0.3139 131 A 0.0461 0.5366 0.4173 132 K 0.0493 0.4513 0.4994 133 D 0.0820 0.2469 0.6711 134 E 0.1430 0.1672 0.6898 135 R 0.4111 0.0969 0.4920 136 V 0.7610 0.0398 0.1991 137 V 0.8399 0.0219 0.1382 138 M 0.8177 0.0207 0.1616 139 V 0.5841 0.0344 0.3815 140 P 0.3967 0.0654 0.5378 141 T 0.3939 0.1824 0.4238 142 V 0.4442 0.2750 0.2807 143 M 0.3914 0.3504 0.2582 144 Y 0.2555 0.5019 0.2427 145 K 0.1173 0.6474 0.2353 146 D 0.0677 0.7291 0.2032 147 M 0.0758 0.7925 0.1318 148 V 0.0737 0.8429 0.0835 149 I 0.0568 0.8783 0.0648 150 K 0.0494 0.8896 0.0610 151 K 0.0476 0.8914 0.0610 152 I 0.0554 0.8737 0.0708 153 I 0.0795 0.8211 0.0994 154 T 0.0848 0.7400 0.1752 155 N 0.0678 0.5453 0.3869 156 T 0.0711 0.4856 0.4433 157 L 0.1155 0.2705 0.6139 158 G 0.1414 0.1011 0.7575 159 L 0.2550 0.0501 0.6950 160 D 0.3444 0.0476 0.6080 161 V 0.2222 0.4322 0.3457 162 E 0.1956 0.4764 0.3280 163 S 0.1802 0.4772 0.3425 164 Q 0.1795 0.3800 0.4404 165 M 0.1820 0.2734 0.5446 166 D 0.0951 0.2515 0.6534 167 G 0.0608 0.2048 0.7344 168 G 0.1358 0.2982 0.5660 169 F 0.3038 0.4695 0.2267 170 L 0.3324 0.5557 0.1119 171 F 0.3107 0.6017 0.0876 172 A 0.3159 0.6065 0.0777 173 M 0.2879 0.6292 0.0829 174 A 0.2766 0.6254 0.0980 175 I 0.2219 0.6540 0.1241 176 A 0.1784 0.6232 0.1984 177 R 0.1178 0.5829 0.2993 178 D 0.0981 0.3481 0.5538 179 A 0.0824 0.2152 0.7024 180 N 0.1090 0.0325 0.8584 181 P 0.0251 0.1666 0.8083 182 R 0.0334 0.1589 0.8077 183 S 0.0754 0.1486 0.7760 184 G 0.0754 0.1008 0.8238 185 S 0.2180 0.1472 0.6349 186 W 0.3010 0.4325 0.2665 187 Y 0.2595 0.5111 0.2294 188 E 0.2875 0.4847 0.2278 189 L 0.2728 0.4499 0.2773 190 A 0.2767 0.2504 0.4730 191 R 0.1979 0.1166 0.6856 192 T 0.0918 0.0272 0.8810 193 P 0.0268 0.5249 0.4483 194 E 0.0186 0.5509 0.4305 195 D 0.0462 0.4939 0.4598 196 L 0.1373 0.1144 0.7483 197 N 0.0973 0.0267 0.8761 198 P 0.0072 0.8434 0.1494 199 E 0.0062 0.8833 0.1104 200 E 0.0085 0.8873 0.1042 201 I 0.0236 0.8207 0.1557 202 G 0.0238 0.6601 0.3161 203 K 0.0218 0.7919 0.1862 204 R 0.0209 0.8486 0.1305 205 A 0.0223 0.8137 0.1640 206 A 0.0163 0.8714 0.1123 207 E 0.0122 0.9133 0.0745 208 E 0.0187 0.9026 0.0787 209 A 0.0296 0.8876 0.0827 210 I 0.0515 0.8575 0.0911 211 S 0.0705 0.8239 0.1056 212 L 0.0919 0.7511 0.1570 213 I 0.1169 0.5857 0.2974 214 G 0.1079 0.2274 0.6647 215 S 0.1224 0.1720 0.7056 216 K 0.1724 0.1371 0.6905 217 T 0.1875 0.0907 0.7218 218 I 0.1213 0.0508 0.8279