# This file is the result of combining several RDB files, specifically # T0301.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0301.t2k.stride-ebghtl.rdb (weight 1.24869) # T0301.t2k.str2.rdb (weight 1.54758) # T0301.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 T0301.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 110 # # ============================================ # Comments from T0301.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 110 # # ============================================ # Comments from T0301.t2k.str2.rdb # ============================================ # TARGET T0301 # 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 T0301.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 110 # # ============================================ # Comments from T0301.t2k.alpha.rdb # ============================================ # TARGET T0301 # 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 T0301.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 110 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0650 0.0669 0.8681 2 G 0.0875 0.0641 0.8484 3 V 0.1595 0.0381 0.8024 4 T 0.2192 0.0635 0.7173 5 F 0.1834 0.0600 0.7566 6 P 0.1915 0.0598 0.7487 7 A 0.2006 0.0574 0.7420 8 A 0.2936 0.0353 0.6711 9 E 0.4841 0.0221 0.4938 10 I 0.7396 0.0134 0.2471 11 V 0.8551 0.0103 0.1345 12 L 0.8474 0.0128 0.1398 13 E 0.8283 0.0136 0.1581 14 F 0.7076 0.0243 0.2681 15 L 0.5091 0.0390 0.4518 16 D 0.3613 0.0362 0.6025 17 P 0.1677 0.2336 0.5987 18 S 0.0790 0.2666 0.6544 19 D 0.0654 0.3574 0.5771 20 D 0.0535 0.2236 0.7229 21 G 0.0745 0.1170 0.8085 22 E 0.1412 0.1186 0.7402 23 D 0.1923 0.1376 0.6701 24 G 0.2105 0.1419 0.6476 25 G 0.1194 0.1164 0.7642 26 A 0.1576 0.1387 0.7037 27 I 0.2529 0.0987 0.6484 28 F 0.1999 0.0455 0.7547 29 P 0.1031 0.0616 0.8353 30 T 0.1029 0.0608 0.8363 31 G 0.1001 0.0477 0.8522 32 N 0.1480 0.0379 0.8141 33 L 0.3155 0.0768 0.6077 34 V 0.5220 0.0822 0.3958 35 D 0.6743 0.0622 0.2635 36 D 0.7804 0.0260 0.1937 37 L 0.8420 0.0140 0.1440 38 E 0.8373 0.0107 0.1520 39 V 0.5906 0.0231 0.3863 40 P 0.0984 0.0694 0.8321 41 G 0.0464 0.0979 0.8557 42 V 0.1133 0.0662 0.8205 43 G 0.2188 0.0460 0.7352 44 T 0.4818 0.0238 0.4944 45 F 0.7573 0.0070 0.2358 46 K 0.8730 0.0064 0.1205 47 A 0.8957 0.0058 0.0985 48 T 0.9111 0.0050 0.0838 49 M 0.9083 0.0072 0.0845 50 I 0.8440 0.0167 0.1392 51 N 0.6416 0.0253 0.3331 52 A 0.3007 0.0717 0.6276 53 G 0.2153 0.0388 0.7459 54 I 0.1834 0.0317 0.7849 55 P 0.2395 0.0202 0.7403 56 T 0.6954 0.0244 0.2802 57 V 0.8626 0.0163 0.1211 58 F 0.9018 0.0111 0.0871 59 V 0.8436 0.0184 0.1381 60 N 0.6285 0.0630 0.3085 61 A 0.0456 0.7004 0.2540 62 E 0.0184 0.7530 0.2286 63 E 0.0186 0.7938 0.1876 64 I 0.0794 0.4649 0.4557 65 G 0.0740 0.1390 0.7869 66 Y 0.1218 0.1202 0.7581 67 R 0.1297 0.0884 0.7818 68 G 0.1094 0.1096 0.7810 69 T 0.1697 0.0780 0.7524 70 E 0.1945 0.0882 0.7173 71 L 0.0889 0.0734 0.8377 72 R 0.0082 0.8465 0.1453 73 E 0.0063 0.8611 0.1326 74 E 0.0083 0.8537 0.1380 75 I 0.0189 0.7567 0.2244 76 N 0.0303 0.5445 0.4252 77 G 0.0267 0.3815 0.5918 78 D 0.0576 0.1491 0.7933 79 P 0.0054 0.9138 0.0808 80 Q 0.0052 0.9333 0.0615 81 Q 0.0049 0.9503 0.0448 82 L 0.0047 0.9581 0.0371 83 A 0.0048 0.9544 0.0408 84 R 0.0047 0.9536 0.0417 85 F 0.0047 0.9565 0.0388 86 E 0.0047 0.9579 0.0374 87 R 0.0047 0.9582 0.0371 88 I 0.0047 0.9598 0.0356 89 R 0.0047 0.9604 0.0350 90 V 0.0047 0.9592 0.0361 91 A 0.0049 0.9560 0.0391 92 G 0.0049 0.9541 0.0410 93 A 0.0049 0.9493 0.0458 94 L 0.0054 0.9392 0.0554 95 R 0.0070 0.9065 0.0865 96 M 0.0437 0.5981 0.3582 97 G 0.0323 0.1178 0.8499 98 L 0.0582 0.1733 0.7685 99 I 0.0793 0.3134 0.6073 100 K 0.0628 0.3528 0.5844 101 T 0.0743 0.3206 0.6051 102 P 0.0209 0.7003 0.2788 103 E 0.0116 0.8418 0.1466 104 E 0.0078 0.8840 0.1082 105 A 0.0109 0.8644 0.1247 106 A 0.0121 0.6761 0.3118 107 T 0.0200 0.3736 0.6063 108 R 0.0707 0.1285 0.8008 109 Q 0.0779 0.0808 0.8413 110 H 0.1215 0.0515 0.8271 111 T 0.2193 0.0158 0.7649 112 P 0.2939 0.0110 0.6951 113 K 0.7594 0.0055 0.2351 114 I 0.8993 0.0041 0.0966 115 A 0.9044 0.0050 0.0906 116 F 0.9127 0.0043 0.0831 117 V 0.8348 0.0125 0.1527 118 A 0.5788 0.0084 0.4128 119 P 0.3151 0.0120 0.6729 120 P 0.1702 0.0579 0.7719 121 R 0.1123 0.1159 0.7718 122 D 0.0855 0.1432 0.7713 123 Y 0.0949 0.1245 0.7807 124 R 0.1645 0.1402 0.6953 125 T 0.2018 0.1383 0.6599 126 A 0.1495 0.1247 0.7258 127 S 0.0958 0.0995 0.8047 128 G 0.0963 0.0617 0.8419 129 K 0.2781 0.0433 0.6787 130 L 0.4761 0.0343 0.4896 131 V 0.4080 0.0428 0.5492 132 A 0.2281 0.0420 0.7300 133 A 0.0601 0.4165 0.5234 134 G 0.0255 0.3426 0.6318 135 D 0.0920 0.2562 0.6518 136 I 0.2917 0.0347 0.6736 137 D 0.4707 0.0346 0.4947 138 L 0.8842 0.0178 0.0979 139 L 0.8990 0.0253 0.0757 140 V 0.8972 0.0265 0.0763 141 R 0.8473 0.0400 0.1127 142 A 0.7056 0.0545 0.2399 143 L 0.4736 0.1009 0.4255 144 S 0.3178 0.0757 0.6065 145 M 0.1062 0.1668 0.7270 146 G 0.0669 0.1323 0.8008 147 K 0.1270 0.1689 0.7041 148 L 0.1061 0.3865 0.5074 149 H 0.0595 0.4590 0.4815 150 H 0.0276 0.6372 0.3351 151 A 0.0184 0.7326 0.2489 152 M 0.0135 0.8409 0.1456 153 M 0.0107 0.9108 0.0785 154 G 0.0088 0.9414 0.0499 155 T 0.0066 0.9525 0.0409 156 A 0.0059 0.9562 0.0378 157 A 0.0053 0.9592 0.0355 158 V 0.0050 0.9596 0.0354 159 A 0.0047 0.9586 0.0366 160 I 0.0052 0.9522 0.0427 161 G 0.0060 0.9457 0.0483 162 T 0.0069 0.9337 0.0594 163 A 0.0078 0.9138 0.0784 164 A 0.0163 0.8145 0.1692 165 A 0.0403 0.5774 0.3822 166 I 0.0835 0.1840 0.7326 167 P 0.0365 0.1873 0.7762 168 G 0.0409 0.1982 0.7609 169 T 0.0920 0.3688 0.5392 170 L 0.0178 0.8871 0.0951 171 V 0.0106 0.9218 0.0676 172 N 0.0094 0.9165 0.0741 173 L 0.0111 0.8974 0.0916 174 A 0.0221 0.8145 0.1634 175 A 0.0478 0.5983 0.3538 176 G 0.0557 0.1954 0.7489 177 G 0.0644 0.0842 0.8514 178 G 0.0662 0.0911 0.8427 179 E 0.0763 0.0943 0.8294 180 R 0.0997 0.0764 0.8239 181 S 0.1947 0.0427 0.7626 182 A 0.5424 0.0162 0.4414 183 V 0.8203 0.0076 0.1720 184 R 0.8544 0.0058 0.1398 185 F 0.7671 0.0151 0.2178 186 G 0.6651 0.0165 0.3184 187 H 0.3119 0.0161 0.6719 188 P 0.1973 0.0513 0.7514 189 S 0.2667 0.0363 0.6970 190 G 0.4948 0.0224 0.4828 191 T 0.7825 0.0061 0.2115 192 L 0.8850 0.0052 0.1099 193 R 0.9146 0.0032 0.0822 194 V 0.9045 0.0058 0.0897 195 G 0.9125 0.0037 0.0837 196 A 0.9097 0.0043 0.0861 197 E 0.9100 0.0039 0.0861 198 A 0.8925 0.0051 0.1024 199 S 0.7726 0.0085 0.2188 200 Q 0.4180 0.0681 0.5139 201 A 0.0981 0.0588 0.8431 202 N 0.0609 0.0519 0.8872 203 G 0.0739 0.0578 0.8684 204 E 0.3972 0.0301 0.5727 205 W 0.7605 0.0080 0.2315 206 T 0.8425 0.0074 0.1501 207 V 0.8989 0.0057 0.0953 208 T 0.8187 0.0293 0.1520 209 K 0.8180 0.0512 0.1309 210 A 0.7331 0.1381 0.1288 211 I 0.7287 0.1512 0.1201 212 M 0.5317 0.3433 0.1250 213 S 0.3053 0.5774 0.1173 214 R 0.1655 0.7268 0.1077 215 S 0.0561 0.8564 0.0875 216 A 0.0309 0.8852 0.0839 217 R 0.0239 0.8717 0.1043 218 I 0.0265 0.8261 0.1473 219 L 0.0388 0.6746 0.2866 220 M 0.1175 0.4282 0.4543 221 E 0.1908 0.2764 0.5328 222 G 0.3238 0.0973 0.5789 223 W 0.5751 0.0562 0.3687 224 V 0.7152 0.0386 0.2461 225 R 0.6793 0.0303 0.2904 226 V 0.5042 0.0242 0.4716 227 P 0.2490 0.0674 0.6836 228 G 0.0325 0.4932 0.4743 229 D 0.0308 0.5131 0.4561 230 A 0.0484 0.4237 0.5278 231 F 0.0391 0.0653 0.8956