# This file is the result of combining several RDB files, specifically # T0360.t06.dssp-ebghstl.rdb (weight 1.53986) # T0360.t06.stride-ebghtl.rdb (weight 1.24869) # T0360.t06.str2.rdb (weight 1.54758) # T0360.t06.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 T0360.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0360 # Using neural net t06-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 T0360.t06-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 49.6402 # # ============================================ # Comments from T0360.t06.stride-ebghtl.rdb # ============================================ # TARGET T0360 # Using neural net t06-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 T0360.t06-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 49.6402 # # ============================================ # Comments from T0360.t06.str2.rdb # ============================================ # TARGET T0360 # Using neural net t06-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 T0360.t06-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 49.6402 # # ============================================ # Comments from T0360.t06.alpha.rdb # ============================================ # TARGET T0360 # Using neural net t06-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 T0360.t06-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 49.6402 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0430 0.0698 0.8873 2 T 0.0494 0.1887 0.7619 3 Q 0.0241 0.5528 0.4231 4 E 0.0318 0.6775 0.2907 5 T 0.0383 0.7368 0.2248 6 A 0.0417 0.7325 0.2258 7 L 0.0412 0.7004 0.2585 8 G 0.0351 0.5271 0.4378 9 A 0.0416 0.5592 0.3992 10 A 0.0623 0.6283 0.3094 11 L 0.0512 0.5999 0.3489 12 K 0.0595 0.5659 0.3746 13 S 0.0742 0.5466 0.3791 14 A 0.0713 0.5406 0.3882 15 V 0.1063 0.4963 0.3974 16 Q 0.1187 0.4258 0.4555 17 T 0.0873 0.3761 0.5366 18 M 0.0559 0.3475 0.5965 19 S 0.0482 0.3246 0.6272 20 K 0.0097 0.8219 0.1684 21 K 0.0066 0.9196 0.0739 22 K 0.0061 0.9385 0.0554 23 Q 0.0049 0.9495 0.0456 24 T 0.0047 0.9555 0.0397 25 E 0.0047 0.9566 0.0387 26 M 0.0047 0.9564 0.0389 27 I 0.0050 0.9505 0.0445 28 A 0.0048 0.9512 0.0441 29 D 0.0052 0.9341 0.0607 30 H 0.0073 0.8775 0.1152 31 I 0.0146 0.7558 0.2296 32 Y 0.0149 0.6295 0.3557 33 G 0.0156 0.4638 0.5206 34 K 0.0400 0.4584 0.5016 35 Y 0.1111 0.1498 0.7391 36 D 0.0875 0.1294 0.7831 37 V 0.0553 0.2526 0.6921 38 F 0.0586 0.2719 0.6695 39 K 0.0659 0.2394 0.6946 40 R 0.0957 0.1571 0.7472 41 F 0.1873 0.0853 0.7274 42 K 0.2326 0.0542 0.7132 43 P 0.2432 0.1228 0.6341 44 L 0.2155 0.2222 0.5623 45 A 0.2874 0.2760 0.4366 46 L 0.2879 0.2906 0.4215 47 G 0.2537 0.2289 0.5174 48 I 0.1321 0.4671 0.4008 49 D 0.0342 0.7512 0.2146 50 Q 0.0065 0.9097 0.0839 51 D 0.0058 0.9343 0.0599 52 L 0.0058 0.9355 0.0587 53 I 0.0059 0.9208 0.0733 54 A 0.0065 0.8300 0.1635 55 A 0.0121 0.6168 0.3711 56 L 0.0656 0.0863 0.8480 57 P 0.0133 0.2312 0.7555 58 Q 0.0213 0.1447 0.8340 59 Y 0.0779 0.0481 0.8740 60 D 0.0683 0.0290 0.9027 61 A 0.0049 0.9465 0.0486 62 A 0.0047 0.9568 0.0385 63 L 0.0047 0.9593 0.0360 64 I 0.0047 0.9606 0.0347 65 A 0.0046 0.9613 0.0341 66 R 0.0046 0.9602 0.0351 67 V 0.0047 0.9592 0.0362 68 L 0.0048 0.9548 0.0404 69 A 0.0051 0.9400 0.0549 70 N 0.0075 0.8515 0.1410 71 H 0.0134 0.6529 0.3336 72 C 0.0509 0.3657 0.5834 73 R 0.0325 0.1870 0.7805 74 R 0.0631 0.1198 0.8171 75 P 0.0071 0.8757 0.1173 76 R 0.0081 0.9043 0.0876 77 Y 0.0117 0.9098 0.0785 78 L 0.0146 0.9121 0.0733 79 K 0.0168 0.8849 0.0983 80 A 0.0374 0.8465 0.1161 81 L 0.0909 0.7762 0.1329 82 A 0.1118 0.6221 0.2661 83 R 0.0331 0.2418 0.7251 84 G 0.0273 0.0328 0.9399 85 G 0.1268 0.0161 0.8571 86 K 0.4449 0.0076 0.5475 87 R 0.8288 0.0077 0.1635 88 F 0.8274 0.0086 0.1639 89 D 0.6511 0.0112 0.3377 90 L 0.2224 0.1167 0.6609 91 N 0.0759 0.0360 0.8880 92 N 0.0768 0.0375 0.8857 93 R 0.2372 0.0272 0.7355 94 F 0.4764 0.0256 0.4980 95 K 0.3402 0.0557 0.6041 96 G 0.3718 0.0366 0.5916 97 E 0.4274 0.0221 0.5504 98 V 0.2767 0.0177 0.7056 99 T 0.0933 0.0194 0.8874 100 P 0.0048 0.9296 0.0655 101 E 0.0047 0.9420 0.0533 102 E 0.0049 0.9514 0.0437 103 Q 0.0047 0.9558 0.0395 104 A 0.0047 0.9477 0.0476 105 I 0.0048 0.9231 0.0721 106 A 0.0053 0.8788 0.1159 107 Q 0.0061 0.7386 0.2553 108 N 0.0105 0.5256 0.4639 109 H 0.0375 0.2223 0.7402 110 P 0.0085 0.6351 0.3564 111 F 0.0084 0.8143 0.1773 112 V 0.0079 0.8847 0.1074 113 Q 0.0054 0.9255 0.0690 114 Q 0.0050 0.9451 0.0499 115 A 0.0050 0.9451 0.0500 116 L 0.0047 0.9405 0.0548 117 Q 0.0047 0.9334 0.0619 118 Q 0.0047 0.9312 0.0641 119 Q 0.0048 0.9208 0.0744 120 S 0.0048 0.9140 0.0812 121 A 0.0048 0.9158 0.0794 122 Q 0.0048 0.9210 0.0742 123 A 0.0049 0.9178 0.0773 124 A 0.0050 0.9079 0.0871 125 A 0.0059 0.8534 0.1406 126 E 0.0061 0.7877 0.2062 127 T 0.0078 0.6694 0.3229 128 L 0.0205 0.4806 0.4988 129 S 0.0218 0.4713 0.5069 130 V 0.0106 0.7179 0.2715 131 E 0.0120 0.7810 0.2070 132 A 0.0088 0.8414 0.1498 133 E 0.0100 0.8613 0.1287 134 A 0.0125 0.8282 0.1593 135 A 0.0204 0.7279 0.2516 136 E 0.0257 0.6185 0.3558 137 S 0.0334 0.4738 0.4928 138 S 0.0301 0.3231 0.6467 139 A 0.0379 0.2060 0.7561 140 A 0.0377 0.1187 0.8437 141 E 0.0322 0.0648 0.9030