# This file is the result of combining several RDB files, specifically # T0300.t06.dssp-ebghstl.rdb (weight 1.53986) # T0300.t06.stride-ebghtl.rdb (weight 1.24869) # T0300.t06.str2.rdb (weight 1.54758) # T0300.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 T0300.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.85162 # # ============================================ # Comments from T0300.t06.stride-ebghtl.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.85162 # # ============================================ # Comments from T0300.t06.str2.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.85162 # # ============================================ # Comments from T0300.t06.alpha.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.85162 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0515 0.1413 0.8072 2 A 0.0598 0.1805 0.7598 3 S 0.0550 0.1251 0.8199 4 K 0.0587 0.0818 0.8594 5 K 0.0587 0.0292 0.9121 6 P 0.0401 0.0871 0.8728 7 D 0.0683 0.0517 0.8800 8 K 0.1005 0.0378 0.8616 9 T 0.1036 0.0257 0.8707 10 Y 0.0048 0.9508 0.0444 11 E 0.0047 0.9602 0.0352 12 E 0.0047 0.9599 0.0354 13 M 0.0047 0.9595 0.0358 14 V 0.0047 0.9601 0.0352 15 K 0.0046 0.9593 0.0360 16 E 0.0047 0.9572 0.0381 17 V 0.0047 0.9581 0.0372 18 E 0.0048 0.9544 0.0408 19 R 0.0047 0.9491 0.0462 20 L 0.0049 0.9473 0.0478 21 K 0.0051 0.9476 0.0473 22 L 0.0054 0.9450 0.0496 23 E 0.0076 0.9244 0.0680 24 N 0.0275 0.8939 0.0786 25 K 0.0048 0.9502 0.0451 26 T 0.0047 0.9491 0.0462 27 L 0.0048 0.9499 0.0453 28 K 0.0047 0.9513 0.0440 29 Q 0.0054 0.9452 0.0495 30 K 0.0062 0.9386 0.0552 31 V 0.0135 0.9016 0.0849 32 K 0.0201 0.8109 0.1689 33 S 0.0263 0.6197 0.3541 34 S 0.0559 0.2079 0.7362 35 G 0.0437 0.0814 0.8749 36 A 0.0995 0.0521 0.8484 37 V 0.1452 0.0333 0.8215 38 S 0.0847 0.0253 0.8900 39 S 0.0492 0.0989 0.8519 40 D 0.0416 0.1355 0.8229 41 D 0.0552 0.2066 0.7383 42 S 0.1149 0.1877 0.6974 43 I 0.2434 0.1292 0.6274 44 L 0.2159 0.0516 0.7325 45 T 0.0815 0.0274 0.8910 46 A 0.0072 0.8980 0.0948 47 A 0.0067 0.9170 0.0763 48 K 0.0067 0.9275 0.0658 49 R 0.0083 0.9312 0.0605 50 E 0.0170 0.9199 0.0631 51 S 0.0240 0.9176 0.0584 52 I 0.0181 0.9311 0.0508 53 I 0.0220 0.9201 0.0579 54 V 0.0164 0.9089 0.0746 55 S 0.0149 0.8827 0.1023 56 S 0.0092 0.8855 0.1053 57 S 0.0087 0.8963 0.0950 58 R 0.0064 0.8973 0.0964 59 A 0.0053 0.9042 0.0904 60 L 0.0049 0.9133 0.0818 61 G 0.0049 0.9301 0.0650 62 A 0.0047 0.9545 0.0408 63 V 0.0047 0.9569 0.0384 64 A 0.0048 0.9547 0.0405 65 M 0.0047 0.9585 0.0368 66 R 0.0047 0.9597 0.0357 67 K 0.0047 0.9589 0.0364 68 I 0.0047 0.9581 0.0371 69 E 0.0047 0.9584 0.0369 70 A 0.0047 0.9568 0.0385 71 K 0.0048 0.9528 0.0424 72 V 0.0054 0.9430 0.0516 73 R 0.0063 0.9167 0.0770 74 S 0.0083 0.8602 0.1315 75 R 0.0110 0.7649 0.2241 76 A 0.0284 0.6538 0.3178 77 A 0.0377 0.4783 0.4840 78 K 0.0585 0.3648 0.5767 79 A 0.0833 0.1771 0.7395 80 V 0.1378 0.0917 0.7705 81 T 0.0772 0.0461 0.8767 82 E 0.0052 0.9465 0.0483 83 Q 0.0047 0.9540 0.0413 84 E 0.0048 0.9549 0.0403 85 L 0.0048 0.9566 0.0386 86 T 0.0047 0.9579 0.0374 87 S 0.0048 0.9510 0.0441 88 L 0.0054 0.9398 0.0548 89 L 0.0124 0.8921 0.0955 90 Q 0.0156 0.6487 0.3358 91 S 0.0311 0.3043 0.6646 92 L 0.1640 0.0514 0.7847 93 T 0.3951 0.0322 0.5727 94 L 0.8594 0.0058 0.1348 95 R 0.9134 0.0037 0.0830 96 V 0.8971 0.0036 0.0994 97 D 0.8690 0.0037 0.1273 98 V 0.7357 0.0079 0.2565 99 S 0.5197 0.0119 0.4684 100 M 0.2517 0.0784 0.6699 101 E 0.1091 0.0646 0.8264 102 E 0.0459 0.0746 0.8795