# This file is the result of combining several RDB files, specifically # T0318.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0318.t2k.stride-ebghtl.rdb (weight 1.24869) # T0318.t2k.str2.rdb (weight 1.54758) # T0318.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 T0318.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0318 # 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 T0318.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 15 # # ============================================ # Comments from T0318.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0318 # 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 T0318.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 15 # # ============================================ # Comments from T0318.t2k.str2.rdb # ============================================ # TARGET T0318 # 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 T0318.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 15 # # ============================================ # Comments from T0318.t2k.alpha.rdb # ============================================ # TARGET T0318 # 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 T0318.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 15 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1220 0.0211 0.8569 2 T 0.4403 0.0207 0.5390 3 Q 0.7556 0.0172 0.2273 4 V 0.8491 0.0161 0.1348 5 L 0.8671 0.0142 0.1187 6 V 0.7646 0.0234 0.2119 7 R 0.3956 0.0711 0.5333 8 N 0.1265 0.1728 0.7007 9 G 0.0749 0.2241 0.7010 10 I 0.1155 0.2262 0.6583 11 Q 0.1132 0.1996 0.6872 12 A 0.1284 0.1803 0.6913 13 V 0.1193 0.0986 0.7821 14 G 0.0795 0.0486 0.8720 15 D 0.0320 0.1692 0.7988 16 G 0.0501 0.1236 0.8263 17 L 0.1736 0.0529 0.7736 18 T 0.2459 0.0126 0.7415 19 S 0.5174 0.0091 0.4735 20 L 0.8962 0.0059 0.0979 21 I 0.9219 0.0062 0.0719 22 I 0.9152 0.0067 0.0781 23 V 0.7801 0.0352 0.1848 24 G 0.4760 0.0363 0.4877 25 K 0.2891 0.1056 0.6053 26 K 0.1889 0.2708 0.5403 27 S 0.1088 0.3719 0.5193 28 V 0.0930 0.4269 0.4802 29 L 0.0932 0.4510 0.4558 30 K 0.1012 0.3128 0.5860 31 N 0.1866 0.1722 0.6412 32 V 0.2305 0.0368 0.7327 33 T 0.1687 0.0329 0.7984 34 F 0.0670 0.6402 0.2928 35 E 0.0291 0.7302 0.2407 36 G 0.0376 0.7324 0.2300 37 K 0.0641 0.6528 0.2831 38 F 0.0770 0.5306 0.3924 39 K 0.0663 0.4336 0.5002 40 E 0.1134 0.3943 0.4923 41 V 0.2073 0.3317 0.4610 42 A 0.1455 0.2404 0.6142 43 Q 0.1118 0.3683 0.5200 44 K 0.1451 0.4071 0.4478 45 F 0.1935 0.3128 0.4937 46 V 0.1065 0.3161 0.5774 47 T 0.0308 0.7455 0.2237 48 D 0.0195 0.8442 0.1363 49 G 0.0119 0.8766 0.1114 50 D 0.0126 0.8981 0.0893 51 S 0.0173 0.9038 0.0789 52 W 0.0148 0.9113 0.0739 53 N 0.0203 0.9016 0.0781 54 S 0.0284 0.8574 0.1142 55 M 0.0400 0.7697 0.1903 56 I 0.0601 0.6562 0.2837 57 S 0.1110 0.3484 0.5406 58 R 0.1092 0.0660 0.8249 59 I 0.1024 0.0549 0.8427 60 P 0.1000 0.0357 0.8643 61 A 0.0398 0.1514 0.8088 62 S 0.0560 0.0908 0.8532 63 G 0.0393 0.1205 0.8402 64 R 0.0864 0.1869 0.7266 65 H 0.1743 0.2324 0.5934 66 P 0.2438 0.3252 0.4310 67 L 0.2576 0.4505 0.2919 68 H 0.3477 0.4176 0.2347 69 Y 0.2963 0.4633 0.2404 70 E 0.2316 0.4670 0.3014 71 L 0.2679 0.4864 0.2457 72 A 0.3510 0.4234 0.2256 73 H 0.4223 0.3794 0.1983 74 L 0.5146 0.3556 0.1298 75 I 0.5317 0.2781 0.1902 76 T 0.5208 0.1795 0.2997 77 V 0.2920 0.0479 0.6601 78 P 0.1739 0.1160 0.7101 79 D 0.0728 0.2064 0.7208 80 A 0.1432 0.2295 0.6273 81 S 0.1699 0.1418 0.6883 82 S 0.1288 0.1088 0.7624 83 R 0.0670 0.1519 0.7811 84 G 0.0536 0.1229 0.8235 85 N 0.0822 0.0900 0.8278 86 T 0.0847 0.0795 0.8359 87 P 0.0364 0.3674 0.5962 88 T 0.0322 0.4658 0.5020 89 N 0.0170 0.7388 0.2442 90 A 0.0126 0.8366 0.1508 91 H 0.0184 0.8322 0.1494 92 S 0.0342 0.8542 0.1116 93 I 0.0333 0.8586 0.1081 94 Y 0.0456 0.8347 0.1197 95 K 0.0500 0.8299 0.1201 96 E 0.0752 0.7697 0.1551 97 L 0.1017 0.7065 0.1919 98 K 0.1259 0.5574 0.3167 99 P 0.1684 0.3623 0.4693 100 I 0.1727 0.1922 0.6352 101 N 0.1480 0.0795 0.7726 102 Y 0.1007 0.0861 0.8132 103 P 0.0784 0.1504 0.7712 104 E 0.0683 0.1981 0.7336 105 D 0.0836 0.1846 0.7318 106 T 0.1655 0.1335 0.7011 107 K 0.2477 0.0586 0.6937 108 N 0.3725 0.0304 0.5970 109 V 0.5874 0.0134 0.3993 110 H 0.8364 0.0059 0.1577 111 F 0.9192 0.0036 0.0772 112 V 0.9278 0.0036 0.0686 113 L 0.9235 0.0036 0.0729 114 F 0.8935 0.0080 0.0985 115 A 0.7435 0.0156 0.2409 116 E 0.3724 0.0261 0.6015 117 Y 0.1171 0.1047 0.7782 118 P 0.0237 0.4131 0.5632 119 D 0.0251 0.5244 0.4505 120 V 0.0401 0.7467 0.2132 121 L 0.0187 0.8724 0.1088 122 S 0.0094 0.9271 0.0635 123 H 0.0084 0.9386 0.0530 124 V 0.0059 0.9505 0.0436 125 A 0.0086 0.9492 0.0423 126 A 0.0082 0.9433 0.0486 127 I 0.0070 0.9424 0.0506 128 A 0.0077 0.9252 0.0671 129 R 0.0095 0.8609 0.1295 130 T 0.0200 0.7792 0.2008 131 F 0.0604 0.5622 0.3774 132 C 0.0427 0.4955 0.4618 133 K 0.0433 0.5366 0.4200 134 F 0.1286 0.4224 0.4490 135 S 0.1452 0.2953 0.5595 136 M 0.1276 0.2327 0.6397 137 K 0.1187 0.1949 0.6864 138 T 0.1105 0.1462 0.7433 139 S 0.0849 0.1327 0.7824 140 G 0.0864 0.1604 0.7532 141 I 0.1096 0.1587 0.7317 142 R 0.1576 0.1618 0.6806 143 E 0.2459 0.1464 0.6077 144 L 0.2409 0.1487 0.6104 145 N 0.2273 0.0665 0.7062 146 V 0.2230 0.0513 0.7256 147 N 0.2814 0.0298 0.6888 148 I 0.4770 0.0192 0.5038 149 D 0.6335 0.0138 0.3528 150 V 0.8671 0.0060 0.1268 151 V 0.9085 0.0053 0.0861 152 C 0.9073 0.0049 0.0878 153 D 0.8723 0.0064 0.1213 154 K 0.8104 0.0079 0.1818 155 L 0.6914 0.0128 0.2958 156 T 0.4703 0.0284 0.5012 157 N 0.1987 0.0367 0.7645 158 E 0.0810 0.0846 0.8344 159 D 0.0854 0.0775 0.8371 160 A 0.0863 0.1008 0.8128 161 V 0.1164 0.1202 0.7635 162 F 0.1585 0.2839 0.5576 163 L 0.1267 0.4497 0.4236 164 T 0.1168 0.5577 0.3255 165 D 0.0815 0.6991 0.2194 166 L 0.0575 0.7421 0.2004 167 S 0.0363 0.8291 0.1346 168 E 0.0113 0.9306 0.0581 169 S 0.0143 0.9297 0.0560 170 V 0.0091 0.9414 0.0495 171 R 0.0096 0.9396 0.0508 172 E 0.0117 0.9274 0.0608 173 T 0.0125 0.8854 0.1022 174 A 0.0316 0.7865 0.1818 175 R 0.0496 0.6760 0.2744 176 L 0.0663 0.4680 0.4656 177 I 0.0391 0.0745 0.8863