# This file is the result of combining several RDB files, specifically # T0293.t04.dssp-ebghstl.rdb (weight 1.53986) # T0293.t04.stride-ebghtl.rdb (weight 1.24869) # T0293.t04.str2.rdb (weight 1.54758) # T0293.t04.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.t04.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.t04-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 4.79834 # # ============================================ # Comments from T0293.t04.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.t04-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 4.79834 # # ============================================ # Comments from T0293.t04.str2.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-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 T0293.t04-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 4.79834 # # ============================================ # Comments from T0293.t04.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.t04-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 4.79834 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.1750 0.0079 0.8171 2 S 0.4782 0.0100 0.5118 3 L 0.4722 0.0162 0.5116 4 N 0.4343 0.0252 0.5405 5 F 0.1860 0.1004 0.7136 6 K 0.1008 0.0631 0.8361 7 D 0.0835 0.0249 0.8916 8 P 0.0055 0.9098 0.0846 9 E 0.0049 0.9469 0.0482 10 A 0.0048 0.9568 0.0384 11 V 0.0047 0.9586 0.0367 12 R 0.0047 0.9590 0.0363 13 A 0.0048 0.9555 0.0398 14 L 0.0047 0.9562 0.0391 15 T 0.0048 0.9538 0.0414 16 C 0.0047 0.9560 0.0393 17 T 0.0050 0.9492 0.0458 18 L 0.0064 0.9187 0.0749 19 L 0.0190 0.8677 0.1133 20 R 0.0233 0.8235 0.1532 21 E 0.0097 0.7597 0.2306 22 D 0.0200 0.5997 0.3803 23 F 0.0822 0.2800 0.6378 24 G 0.1206 0.0291 0.8503 25 L 0.2689 0.0097 0.7215 26 S 0.6080 0.0104 0.3815 27 I 0.7538 0.0070 0.2392 28 D 0.7677 0.0063 0.2260 29 I 0.5145 0.0086 0.4769 30 P 0.2085 0.0162 0.7754 31 L 0.0265 0.5867 0.3868 32 E 0.0153 0.5992 0.3855 33 R 0.0438 0.6181 0.3381 34 L 0.2370 0.2259 0.5370 35 I 0.1904 0.0975 0.7121 36 P 0.2076 0.0850 0.7074 37 T 0.2272 0.0851 0.6877 38 V 0.1670 0.0548 0.7782 39 P 0.1662 0.0906 0.7432 40 L 0.2188 0.1414 0.6397 41 R 0.3781 0.1238 0.4981 42 L 0.4961 0.0827 0.4213 43 N 0.4872 0.0866 0.4262 44 Y 0.7742 0.0706 0.1552 45 I 0.8643 0.0391 0.0966 46 H 0.8855 0.0257 0.0888 47 W 0.8289 0.0304 0.1407 48 V 0.5199 0.0410 0.4391 49 E 0.2734 0.0425 0.6841