# This file is the result of combining several RDB files, specifically # T0335.t06.dssp-ebghstl.rdb (weight 1.53986) # T0335.t06.stride-ebghtl.rdb (weight 1.24869) # T0335.t06.str2.rdb (weight 1.54758) # T0335.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 T0335.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t06.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0279 0.1529 0.8192 2 I 0.0541 0.2867 0.6593 3 S 0.0393 0.4940 0.4667 4 N 0.0138 0.8072 0.1790 5 A 0.0105 0.8913 0.0982 6 K 0.0065 0.9365 0.0570 7 I 0.0050 0.9482 0.0468 8 A 0.0047 0.9539 0.0413 9 R 0.0047 0.9545 0.0408 10 I 0.0047 0.9564 0.0389 11 N 0.0047 0.9565 0.0388 12 E 0.0047 0.9545 0.0408 13 L 0.0048 0.9405 0.0547 14 A 0.0048 0.9188 0.0764 15 A 0.0055 0.8730 0.1215 16 K 0.0084 0.8233 0.1683 17 A 0.0146 0.7689 0.2166 18 K 0.0167 0.7327 0.2506 19 A 0.0314 0.5667 0.4019 20 G 0.0325 0.2587 0.7088 21 V 0.0445 0.1191 0.8364 22 I 0.1023 0.0303 0.8673 23 T 0.0541 0.0223 0.9236 24 E 0.0048 0.9460 0.0492 25 E 0.0047 0.9515 0.0438 26 E 0.0049 0.9532 0.0420 27 K 0.0047 0.9589 0.0365 28 A 0.0046 0.9591 0.0363 29 E 0.0046 0.9556 0.0397 30 Q 0.0047 0.9577 0.0377 31 Q 0.0046 0.9577 0.0376 32 K 0.0047 0.9525 0.0429 33 L 0.0047 0.9495 0.0458 34 R 0.0047 0.9578 0.0376 35 Q 0.0047 0.9603 0.0350 36 E 0.0049 0.9568 0.0384 37 Y 0.0048 0.9544 0.0408 38 L 0.0047 0.9561 0.0392 39 K 0.0049 0.9548 0.0403 40 G 0.0049 0.9453 0.0497 41 F 0.0053 0.9412 0.0535 42 R 0.0052 0.9462 0.0486 43 S 0.0051 0.9428 0.0521 44 S 0.0050 0.9324 0.0626 45 M 0.0053 0.9309 0.0638 46 K 0.0062 0.9185 0.0753 47 N 0.0095 0.8739 0.1166 48 T 0.0147 0.7738 0.2115 49 L 0.0789 0.6074 0.3137 50 K 0.1150 0.3542 0.5308 51 S 0.1923 0.2469 0.5607 52 V 0.5672 0.0530 0.3799 53 K 0.8146 0.0210 0.1644 54 I 0.8794 0.0084 0.1122 55 I 0.7815 0.0107 0.2078 56 D 0.1726 0.0129 0.8145 57 P 0.0085 0.1335 0.8581 58 E 0.0427 0.0383 0.9190 59 G 0.0545 0.0523 0.8933 60 N 0.0862 0.0639 0.8499 61 D 0.3700 0.0416 0.5884 62 V 0.2611 0.0247 0.7142 63 T 0.0937 0.0168 0.8895 64 P 0.0072 0.9154 0.0774 65 E 0.0047 0.9490 0.0462 66 K 0.0048 0.9515 0.0437 67 L 0.0064 0.9451 0.0485 68 K 0.0056 0.9409 0.0535 69 R 0.0059 0.9336 0.0606 70 E 0.0060 0.9174 0.0766 71 Q 0.0088 0.8903 0.1009 72 R 0.0106 0.8314 0.1580 73 N 0.0141 0.6922 0.2937 74 N 0.0340 0.4703 0.4958 75 K 0.0366 0.4140 0.5494 76 L 0.0736 0.4272 0.4992 77 H 0.0976 0.4297 0.4727 78 L 0.0950 0.4326 0.4724 79 E 0.0795 0.3922 0.5284 80 H 0.0844 0.3295 0.5862 81 H 0.0806 0.3010 0.6184 82 H 0.0732 0.2178 0.7090 83 H 0.0779 0.1459 0.7762 84 H 0.0549 0.1045 0.8405 85 H 0.0445 0.0395 0.9160