# This file is the result of combining several RDB files, specifically # T0342.t06.dssp-ebghstl.rdb (weight 1.53986) # T0342.t06.stride-ebghtl.rdb (weight 1.24869) # T0342.t06.str2.rdb (weight 1.54758) # T0342.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 T0342.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.88164 # # ============================================ # Comments from T0342.t06.stride-ebghtl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.88164 # # ============================================ # Comments from T0342.t06.str2.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.88164 # # ============================================ # Comments from T0342.t06.alpha.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.88164 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.0964 0.0220 0.8815 2 K 0.6792 0.0067 0.3141 3 I 0.9081 0.0040 0.0879 4 I 0.9266 0.0038 0.0696 5 C 0.9122 0.0061 0.0817 6 M 0.7425 0.0433 0.2141 7 G 0.4361 0.0246 0.5393 8 A 0.2523 0.2182 0.5295 9 K 0.1193 0.4327 0.4480 10 E 0.0755 0.4781 0.4465 11 N 0.0579 0.1701 0.7720 12 G 0.0453 0.0268 0.9278 13 L 0.0701 0.0207 0.9091 14 P 0.0730 0.0769 0.8501 15 L 0.0091 0.8721 0.1188 16 E 0.0070 0.9139 0.0791 17 Y 0.0057 0.9339 0.0604 18 Q 0.0055 0.9459 0.0486 19 E 0.0067 0.9360 0.0572 20 K 0.0064 0.9131 0.0805 21 L 0.0130 0.8634 0.1237 22 K 0.0174 0.7608 0.2218 23 A 0.0333 0.6079 0.3588 24 I 0.1206 0.1913 0.6881 25 E 0.1023 0.0371 0.8606 26 P 0.0841 0.1453 0.7706 27 N 0.1018 0.1427 0.7555 28 D 0.0900 0.2117 0.6983 29 Y 0.1435 0.1476 0.7089 30 T 0.1411 0.0990 0.7598 31 G 0.1230 0.0624 0.8146 32 K 0.2374 0.0589 0.7037 33 V 0.1841 0.0577 0.7582 34 S 0.0710 0.0996 0.8293 35 E 0.0078 0.8820 0.1101 36 E 0.0085 0.8946 0.0969 37 I 0.0056 0.9351 0.0593 38 E 0.0060 0.9436 0.0504 39 D 0.0056 0.9449 0.0495 40 I 0.0055 0.9414 0.0531 41 I 0.0098 0.9171 0.0731 42 K 0.0144 0.8511 0.1345 43 K 0.0324 0.5482 0.4194 44 G 0.0338 0.1940 0.7722 45 E 0.0631 0.1906 0.7463 46 T 0.1221 0.1982 0.6797 47 Q 0.1442 0.1617 0.6941 48 T 0.1058 0.0661 0.8282 49 L 0.0472 0.0357 0.9171