# This file is the result of combining several RDB files, specifically # T0344.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0344.t2k.stride-ebghtl.rdb (weight 1.24869) # T0344.t2k.str2.rdb (weight 1.54758) # T0344.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 T0344.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 5 # # ============================================ # Comments from T0344.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 5 # # ============================================ # Comments from T0344.t2k.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 5 # # ============================================ # Comments from T0344.t2k.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1079 0.0164 0.8757 2 R 0.4137 0.0183 0.5680 3 I 0.7855 0.0158 0.1987 4 V 0.8304 0.0293 0.1403 5 A 0.8144 0.0190 0.1665 6 A 0.6717 0.0516 0.2767 7 D 0.4131 0.0571 0.5298 8 T 0.1844 0.0947 0.7208 9 G 0.1221 0.0893 0.7886 10 G 0.1562 0.1449 0.6989 11 A 0.2868 0.1628 0.5504 12 V 0.4791 0.1713 0.3496 13 L 0.4742 0.1661 0.3597 14 D 0.2915 0.1707 0.5378 15 E 0.0936 0.2994 0.6070 16 T 0.0501 0.2458 0.7041 17 F 0.0782 0.1863 0.7355 18 E 0.0985 0.1166 0.7849 19 P 0.2047 0.2099 0.5853 20 I 0.3727 0.2598 0.3675 21 G 0.4837 0.2390 0.2773 22 L 0.6102 0.2564 0.1334 23 I 0.5891 0.3037 0.1072 24 A 0.6147 0.2721 0.1133 25 T 0.6601 0.2257 0.1142 26 V 0.6313 0.2364 0.1323 27 A 0.5770 0.2917 0.1312 28 V 0.5871 0.2825 0.1304 29 L 0.6007 0.2277 0.1716 30 V 0.5250 0.1685 0.3065 31 E 0.3791 0.0921 0.5288 32 K 0.2332 0.0590 0.7078 33 P 0.1694 0.1162 0.7144 34 Y 0.1160 0.1960 0.6880 35 R 0.1395 0.1856 0.6749 36 S 0.1738 0.1755 0.6507 37 A 0.1482 0.3187 0.5331 38 K 0.2305 0.3013 0.4682 39 E 0.4289 0.2049 0.3661 40 V 0.5328 0.1229 0.3442 41 M 0.6990 0.0770 0.2240 42 V 0.7685 0.0599 0.1716 43 K 0.7196 0.0857 0.1947 44 Y 0.5887 0.0679 0.3434 45 A 0.2802 0.0573 0.6625 46 N 0.1377 0.0325 0.8298 47 P 0.0671 0.1804 0.7524 48 Y 0.1016 0.1698 0.7285 49 D 0.1566 0.1442 0.6992 50 Y 0.1412 0.1482 0.7106 51 D 0.1219 0.1498 0.7283 52 L 0.0651 0.2517 0.6832 53 T 0.0552 0.2658 0.6791 54 G 0.0393 0.4616 0.4992 55 R 0.0372 0.6730 0.2897 56 Q 0.0514 0.7577 0.1909 57 A 0.0405 0.7998 0.1597 58 I 0.0246 0.8643 0.1110 59 R 0.0182 0.8838 0.0980 60 D 0.0122 0.8955 0.0923 61 E 0.0071 0.9428 0.0500 62 V 0.0059 0.9549 0.0392 63 L 0.0060 0.9562 0.0378 64 L 0.0065 0.9550 0.0385 65 A 0.0047 0.9554 0.0399 66 I 0.0069 0.9519 0.0412 67 E 0.0085 0.9393 0.0521 68 L 0.0117 0.9089 0.0794 69 A 0.0075 0.9024 0.0901 70 R 0.0130 0.8130 0.1740 71 K 0.0337 0.6108 0.3554 72 V 0.1136 0.2466 0.6398 73 K 0.0778 0.0472 0.8750 74 P 0.0819 0.0691 0.8490 75 D 0.1075 0.1067 0.7858 76 V 0.6623 0.0462 0.2915 77 I 0.8455 0.0198 0.1347 78 H 0.8309 0.0130 0.1561 79 L 0.7034 0.0414 0.2552 80 D 0.3699 0.0622 0.5679 81 S 0.2227 0.1085 0.6688 82 T 0.1951 0.1264 0.6785 83 L 0.1308 0.1515 0.7177 84 G 0.0986 0.0909 0.8105 85 G 0.1980 0.0906 0.7114 86 I 0.5175 0.0901 0.3924 87 E 0.6266 0.1084 0.2650 88 L 0.6166 0.1229 0.2605 89 R 0.5027 0.1844 0.3130 90 K 0.4015 0.1970 0.4015 91 L 0.2676 0.2011 0.5313 92 D 0.1147 0.1494 0.7358 93 E 0.0812 0.2466 0.6722 94 P 0.0810 0.3742 0.5448 95 T 0.0960 0.5279 0.3762 96 I 0.0412 0.7495 0.2094 97 D 0.0445 0.7523 0.2032 98 A 0.0438 0.7325 0.2237 99 L 0.1014 0.4545 0.4442 100 G 0.1367 0.2650 0.5984 101 I 0.1707 0.2245 0.6048 102 S 0.1398 0.1952 0.6650 103 D 0.0393 0.4388 0.5218 104 K 0.0335 0.4478 0.5187 105 G 0.0300 0.3954 0.5747 106 K 0.1206 0.5154 0.3640 107 E 0.1900 0.5972 0.2128 108 V 0.0926 0.7262 0.1813 109 W 0.0375 0.8165 0.1460 110 K 0.0189 0.8461 0.1349 111 E 0.0194 0.8042 0.1764 112 L 0.0268 0.7514 0.2218 113 S 0.0252 0.6495 0.3254 114 K 0.0131 0.5986 0.3883 115 D 0.0237 0.5318 0.4445 116 L 0.0201 0.6950 0.2849 117 Q 0.0098 0.7798 0.2104 118 P 0.0057 0.8900 0.1043 119 L 0.0049 0.9195 0.0756 120 A 0.0049 0.9335 0.0617 121 R 0.0051 0.9293 0.0655 122 K 0.0058 0.9253 0.0689 123 F 0.0084 0.9135 0.0781 124 W 0.0153 0.8801 0.1046 125 E 0.0137 0.8775 0.1087 126 E 0.0276 0.7631 0.2093 127 T 0.0571 0.4358 0.5071 128 N 0.0499 0.0410 0.9092 129 I 0.1862 0.0205 0.7932 130 E 0.6149 0.0085 0.3766 131 I 0.8483 0.0079 0.1438 132 V 0.8916 0.0089 0.0995 133 A 0.8613 0.0105 0.1283 134 I 0.7145 0.0358 0.2498 135 G 0.4943 0.0291 0.4766 136 K 0.2176 0.0893 0.6932 137 S 0.1646 0.1175 0.7179 138 S 0.1846 0.1028 0.7126 139 V 0.2302 0.0784 0.6914 140 P 0.4406 0.1176 0.4418 141 V 0.5384 0.2086 0.2529 142 R 0.6598 0.2145 0.1257 143 I 0.6067 0.3036 0.0897 144 A 0.6102 0.3029 0.0869 145 E 0.5722 0.3312 0.0966 146 I 0.4358 0.4220 0.1422 147 Y 0.2641 0.5226 0.2134 148 A 0.1342 0.5991 0.2666 149 G 0.1094 0.5892 0.3014 150 I 0.0887 0.7460 0.1653 151 Y 0.0923 0.7750 0.1327 152 S 0.0682 0.8131 0.1187 153 A 0.0471 0.8649 0.0880 154 K 0.0259 0.9040 0.0702 155 W 0.0325 0.8900 0.0776 156 G 0.0363 0.8655 0.0982 157 I 0.0273 0.8771 0.0956 158 E 0.0347 0.8541 0.1112 159 N 0.0399 0.8091 0.1510 160 V 0.1409 0.6600 0.1991 161 E 0.1565 0.6007 0.2428 162 K 0.1308 0.5248 0.3444 163 E 0.0888 0.1303 0.7809 164 G 0.0402 0.0316 0.9281 165 H 0.3492 0.0217 0.6291 166 L 0.8678 0.0049 0.1272 167 I 0.9019 0.0068 0.0913 168 I 0.8581 0.0251 0.1168 169 G 0.7082 0.0114 0.2804 170 L 0.3124 0.0186 0.6690 171 P 0.1542 0.0682 0.7776 172 R 0.2096 0.1063 0.6841 173 Y 0.5628 0.0559 0.3813 174 M 0.7175 0.0201 0.2624 175 E 0.8573 0.0088 0.1339 176 V 0.8630 0.0062 0.1308 177 N 0.8582 0.0039 0.1379 178 I 0.7473 0.0070 0.2457 179 K 0.4248 0.0169 0.5583 180 D 0.0663 0.0506 0.8832 181 G 0.0462 0.0423 0.9116 182 K 0.4603 0.0166 0.5231 183 I 0.7602 0.0095 0.2302 184 I 0.6709 0.0353 0.2937 185 G 0.4649 0.0328 0.5023 186 R 0.3526 0.0371 0.6103 187 S 0.3751 0.0352 0.5897 188 L 0.2831 0.0299 0.6871 189 D 0.1804 0.0214 0.7981 190 P 0.0547 0.3031 0.6422 191 R 0.0427 0.2650 0.6923 192 E 0.1115 0.2629 0.6256 193 G 0.1489 0.1259 0.7252 194 G 0.1968 0.0915 0.7117 195 L 0.3891 0.0756 0.5353 196 Y 0.6231 0.0429 0.3341 197 G 0.7070 0.0228 0.2702 198 S 0.8403 0.0089 0.1508 199 A 0.8638 0.0082 0.1280 200 E 0.8927 0.0044 0.1029 201 V 0.8515 0.0062 0.1423 202 S 0.8131 0.0081 0.1788 203 V 0.4986 0.0174 0.4840 204 P 0.1464 0.0616 0.7919 205 E 0.0514 0.0686 0.8800 206 G 0.1007 0.0484 0.8509 207 V 0.3899 0.0093 0.6008 208 K 0.7597 0.0086 0.2318 209 W 0.8652 0.0063 0.1286 210 E 0.8651 0.0082 0.1267 211 I 0.7901 0.0159 0.1940 212 Y 0.4233 0.0148 0.5619 213 P 0.1639 0.0295 0.8067 214 N 0.0897 0.0244 0.8858 215 P 0.0394 0.4106 0.5500 216 V 0.1027 0.4718 0.4255 217 A 0.1913 0.4771 0.3316 218 R 0.3072 0.3893 0.3035 219 R 0.4099 0.2988 0.2912 220 F 0.5224 0.2061 0.2714 221 M 0.7179 0.0837 0.1984 222 I 0.8157 0.0633 0.1209 223 F 0.8369 0.0459 0.1172 224 E 0.8519 0.0262 0.1219 225 I 0.7777 0.0441 0.1782 226 F 0.5838 0.0566 0.3596 227 S 0.3573 0.0507 0.5920 228 K 0.1554 0.0680 0.7766 229 R 0.0417 0.0368 0.9215