# This file is the result of combining several RDB files, specifically # T0293.t06.dssp-ebghstl.rdb (weight 1.53986) # T0293.t06.stride-ebghtl.rdb (weight 1.24869) # T0293.t06.str2.rdb (weight 1.54758) # T0293.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 T0293.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.stride-ebghtl.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.str2.rdb # ============================================ # TARGET T0293 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.alpha.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-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 T0293.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 5.9079 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.2248 0.0108 0.7644 2 S 0.4358 0.0115 0.5527 3 L 0.4934 0.0173 0.4893 4 N 0.3969 0.0237 0.5794 5 F 0.1377 0.1451 0.7173 6 K 0.0551 0.0998 0.8451 7 D 0.0869 0.0504 0.8627 8 P 0.0056 0.9184 0.0761 9 E 0.0049 0.9465 0.0486 10 A 0.0048 0.9561 0.0391 11 V 0.0048 0.9576 0.0376 12 R 0.0047 0.9567 0.0386 13 A 0.0050 0.9477 0.0473 14 L 0.0050 0.9481 0.0468 15 T 0.0058 0.9387 0.0554 16 C 0.0060 0.9280 0.0660 17 T 0.0090 0.9097 0.0813 18 L 0.0166 0.8284 0.1549 19 L 0.0538 0.7221 0.2241 20 R 0.0619 0.5970 0.3410 21 E 0.0268 0.5948 0.3785 22 D 0.0295 0.4812 0.4892 23 F 0.1045 0.2747 0.6208 24 G 0.1588 0.0465 0.7948 25 L 0.2785 0.0132 0.7083 26 S 0.4831 0.0157 0.5013 27 I 0.7063 0.0083 0.2854 28 D 0.7542 0.0093 0.2365 29 I 0.6194 0.0123 0.3682 30 P 0.2630 0.0304 0.7066 31 L 0.0448 0.5070 0.4482 32 E 0.0258 0.5120 0.4622 33 R 0.0623 0.5034 0.4342 34 L 0.2757 0.1572 0.5671 35 I 0.1912 0.0680 0.7409 36 P 0.1736 0.0545 0.7719 37 T 0.1709 0.0547 0.7744 38 V 0.1262 0.0399 0.8339 39 P 0.1070 0.0932 0.7998 40 L 0.1288 0.1504 0.7208 41 R 0.2354 0.1273 0.6373 42 L 0.3158 0.2277 0.4564 43 N 0.3643 0.1951 0.4406 44 Y 0.6326 0.2080 0.1595 45 I 0.6563 0.2460 0.0976 46 H 0.6727 0.2229 0.1044 47 W 0.5589 0.2154 0.2257 48 V 0.3004 0.1346 0.5649 49 E 0.1456 0.0855 0.7689