# This file is the result of combining several RDB files, specifically # T0216.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0216.t2k.stride-ebghtl.rdb (weight 1.24869) # T0216.t2k.str2.rdb (weight 1.54758) # T0216.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 T0216.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 64 # # ============================================ # Comments from T0216.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 64 # # ============================================ # Comments from T0216.t2k.str2.rdb # ============================================ # TARGET T0216 # 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 T0216.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 64 # # ============================================ # Comments from T0216.t2k.alpha.rdb # ============================================ # TARGET T0216 # 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 T0216.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 64 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0549 0.0993 0.8458 2 T 0.0758 0.1602 0.7640 3 F 0.0212 0.6356 0.3432 4 E 0.0071 0.8674 0.1255 5 E 0.0075 0.8875 0.1050 6 F 0.0062 0.9105 0.0833 7 K 0.0049 0.9440 0.0511 8 D 0.0050 0.9468 0.0482 9 R 0.0048 0.9541 0.0411 10 L 0.0048 0.9567 0.0385 11 F 0.0048 0.9582 0.0370 12 A 0.0048 0.9562 0.0390 13 L 0.0048 0.9555 0.0397 14 A 0.0048 0.9520 0.0432 15 K 0.0053 0.9279 0.0668 16 K 0.0093 0.8504 0.1403 17 N 0.0422 0.3462 0.6116 18 G 0.0354 0.0236 0.9410 19 V 0.0756 0.0114 0.9130 20 E 0.2808 0.0122 0.7070 21 V 0.7187 0.0051 0.2762 22 Q 0.8602 0.0040 0.1359 23 I 0.9168 0.0031 0.0801 24 S 0.9183 0.0035 0.0781 25 F 0.9061 0.0038 0.0901 26 L 0.8472 0.0089 0.1439 27 E 0.7337 0.0165 0.2497 28 T 0.4417 0.0373 0.5210 29 R 0.2984 0.0466 0.6550 30 E 0.3769 0.0274 0.5957 31 F 0.6804 0.0106 0.3090 32 S 0.8524 0.0044 0.1432 33 L 0.8960 0.0038 0.1003 34 R 0.9006 0.0036 0.0958 35 L 0.8042 0.0075 0.1882 36 A 0.5801 0.0324 0.3875 37 N 0.0910 0.0329 0.8761 38 G 0.0930 0.0408 0.8662 39 D 0.6902 0.0114 0.2985 40 L 0.8840 0.0039 0.1121 41 D 0.8309 0.0217 0.1474 42 Q 0.8753 0.0076 0.1171 43 Y 0.8539 0.0102 0.1359 44 T 0.8582 0.0093 0.1325 45 D 0.7939 0.0188 0.1873 46 A 0.5176 0.0372 0.4452 47 G 0.2437 0.0596 0.6967 48 K 0.2076 0.0580 0.7344 49 F 0.4364 0.0279 0.5357 50 N 0.7448 0.0118 0.2434 51 V 0.8857 0.0039 0.1104 52 E 0.9109 0.0042 0.0849 53 I 0.9226 0.0032 0.0743 54 K 0.9244 0.0035 0.0721 55 V 0.9211 0.0034 0.0755 56 L 0.9029 0.0056 0.0915 57 K 0.7423 0.0202 0.2375 58 D 0.1153 0.0280 0.8567 59 G 0.0751 0.0436 0.8813 60 K 0.5599 0.0282 0.4119 61 T 0.8716 0.0071 0.1213 62 G 0.8805 0.0068 0.1127 63 T 0.9057 0.0061 0.0882 64 F 0.8468 0.0177 0.1355 65 R 0.7286 0.0175 0.2538 66 T 0.3591 0.0731 0.5678 67 Q 0.1006 0.1176 0.7818 68 V 0.1018 0.0869 0.8113 69 L 0.0189 0.5434 0.4377 70 E 0.0128 0.6877 0.2995 71 N 0.0129 0.7583 0.2287 72 P 0.0052 0.9268 0.0680 73 E 0.0050 0.9499 0.0451 74 K 0.0048 0.9528 0.0424 75 C 0.0048 0.9573 0.0379 76 F 0.0047 0.9584 0.0369 77 E 0.0048 0.9586 0.0366 78 E 0.0048 0.9575 0.0377 79 A 0.0048 0.9552 0.0400 80 L 0.0050 0.9523 0.0427 81 S 0.0051 0.9397 0.0551 82 N 0.0062 0.9135 0.0803 83 L 0.0110 0.8708 0.1182 84 Q 0.0121 0.8023 0.1856 85 V 0.0234 0.6578 0.3189 86 K 0.0609 0.3472 0.5919 87 D 0.0667 0.1457 0.7876 88 S 0.0303 0.2515 0.7182 89 E 0.0536 0.2162 0.7302 90 E 0.0602 0.3324 0.6074 91 K 0.0963 0.3321 0.5716 92 E 0.1266 0.3035 0.5699 93 Y 0.1342 0.2309 0.6348 94 F 0.1414 0.2215 0.6371 95 F 0.1360 0.2352 0.6288 96 E 0.1100 0.2504 0.6396 97 G 0.0624 0.3651 0.5724 98 G 0.0831 0.3067 0.6102 99 K 0.0923 0.2763 0.6314 100 E 0.0978 0.1996 0.7026 101 Y 0.1071 0.1705 0.7224 102 R 0.1137 0.1437 0.7426 103 E 0.1068 0.1379 0.7554 104 M 0.1118 0.2068 0.6814 105 E 0.1341 0.2462 0.6198 106 T 0.1123 0.3629 0.5248 107 Y 0.1303 0.3298 0.5399 108 V 0.1257 0.2512 0.6231 109 G 0.1039 0.1417 0.7544 110 R 0.1004 0.0710 0.8287 111 F 0.0346 0.5850 0.3804 112 E 0.0234 0.5515 0.4250 113 K 0.0571 0.4329 0.5100 114 L 0.1521 0.0317 0.8162 115 S 0.0647 0.0178 0.9176 116 V 0.0054 0.9087 0.0859 117 K 0.0049 0.9352 0.0599 118 E 0.0050 0.9376 0.0574 119 K 0.0048 0.9504 0.0447 120 M 0.0048 0.9534 0.0419 121 D 0.0048 0.9527 0.0425 122 M 0.0048 0.9513 0.0440 123 A 0.0047 0.9552 0.0401 124 K 0.0048 0.9551 0.0400 125 K 0.0048 0.9545 0.0407 126 A 0.0048 0.9531 0.0422 127 H 0.0048 0.9534 0.0418 128 E 0.0051 0.9426 0.0523 129 S 0.0055 0.9199 0.0746 130 A 0.0081 0.8657 0.1262 131 A 0.0101 0.7155 0.2745 132 K 0.0220 0.4772 0.5008 133 D 0.0692 0.1337 0.7972 134 E 0.0234 0.2146 0.7619 135 R 0.0958 0.2255 0.6787 136 V 0.3726 0.1488 0.4786 137 V 0.6326 0.0612 0.3062 138 M 0.6749 0.0328 0.2923 139 V 0.5516 0.0200 0.4284 140 P 0.5040 0.0419 0.4541 141 T 0.5675 0.0398 0.3926 142 V 0.6984 0.0259 0.2757 143 M 0.7557 0.0225 0.2218 144 Y 0.6859 0.0401 0.2739 145 K 0.4994 0.0607 0.4399 146 D 0.3255 0.1527 0.5218 147 M 0.4262 0.1406 0.4332 148 V 0.6604 0.0923 0.2473 149 I 0.8038 0.0403 0.1559 150 K 0.8820 0.0188 0.0992 151 K 0.9036 0.0177 0.0786 152 I 0.9039 0.0193 0.0768 153 I 0.8964 0.0220 0.0816 154 T 0.8484 0.0337 0.1179 155 N 0.6337 0.0518 0.3145 156 T 0.2905 0.0800 0.6295 157 L 0.1248 0.0750 0.8002 158 G 0.1734 0.0870 0.7395 159 L 0.4447 0.0763 0.4791 160 D 0.6364 0.0674 0.2962 161 V 0.5745 0.0907 0.3348 162 E 0.4943 0.0894 0.4163 163 S 0.4520 0.0660 0.4820 164 Q 0.4412 0.0725 0.4863 165 M 0.4672 0.0430 0.4897 166 D 0.5308 0.0472 0.4220 167 G 0.7138 0.0303 0.2560 168 G 0.8650 0.0090 0.1259 169 F 0.9044 0.0052 0.0903 170 L 0.9192 0.0040 0.0768 171 F 0.9210 0.0038 0.0751 172 A 0.9256 0.0031 0.0713 173 M 0.9241 0.0038 0.0722 174 A 0.9201 0.0039 0.0760 175 I 0.9132 0.0054 0.0814 176 A 0.7754 0.0129 0.2117 177 R 0.2611 0.0418 0.6971 178 D 0.0579 0.0447 0.8974 179 A 0.1430 0.0583 0.7987 180 N 0.5071 0.0435 0.4494 181 P 0.7711 0.0291 0.1998 182 R 0.7244 0.0482 0.2274 183 S 0.5976 0.0795 0.3229 184 G 0.4129 0.1050 0.4821 185 S 0.3668 0.1335 0.4997 186 W 0.3878 0.1536 0.4586 187 Y 0.3761 0.1543 0.4696 188 E 0.2802 0.2224 0.4974 189 L 0.1743 0.2406 0.5851 190 A 0.1313 0.1977 0.6710 191 R 0.1122 0.1979 0.6899 192 T 0.1058 0.1788 0.7154 193 P 0.0864 0.3382 0.5753 194 E 0.1118 0.3198 0.5684 195 D 0.1478 0.2345 0.6177 196 L 0.1608 0.0570 0.7821 197 N 0.0927 0.0350 0.8723 198 P 0.0066 0.8871 0.1063 199 E 0.0055 0.9071 0.0874 200 E 0.0055 0.9263 0.0682 201 I 0.0053 0.9278 0.0669 202 G 0.0053 0.9292 0.0655 203 K 0.0053 0.9311 0.0636 204 R 0.0052 0.9375 0.0573 205 A 0.0048 0.9502 0.0450 206 A 0.0048 0.9529 0.0422 207 E 0.0050 0.9491 0.0459 208 E 0.0048 0.9547 0.0405 209 A 0.0047 0.9558 0.0395 210 I 0.0050 0.9475 0.0475 211 S 0.0056 0.9259 0.0685 212 L 0.0073 0.8555 0.1372 213 I 0.0492 0.4597 0.4911 214 G 0.0477 0.0521 0.9002 215 S 0.0739 0.0296 0.8965 216 K 0.1610 0.0426 0.7964 217 T 0.1913 0.0270 0.7817 218 I 0.0642 0.0211 0.9148