# This file is the result of combining several RDB files, specifically # T0342.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0342.t2k.stride-ebghtl.rdb (weight 1.24869) # T0342.t2k.str2.rdb (weight 1.54758) # T0342.t2k.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.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0342 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0342.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9 # # ============================================ # Comments from T0342.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0342 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0342.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9 # # ============================================ # Comments from T0342.t2k.str2.rdb # ============================================ # TARGET T0342 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0342.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9 # # ============================================ # Comments from T0342.t2k.alpha.rdb # ============================================ # TARGET T0342 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0342.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.1820 0.0280 0.7900 2 K 0.5577 0.0097 0.4326 3 I 0.8481 0.0116 0.1403 4 I 0.7899 0.0209 0.1892 5 C 0.6733 0.0332 0.2935 6 M 0.3387 0.1593 0.5019 7 G 0.2164 0.2710 0.5127 8 A 0.1200 0.4606 0.4194 9 K 0.0620 0.5849 0.3531 10 E 0.0395 0.5530 0.4076 11 N 0.0556 0.2122 0.7322 12 G 0.0540 0.0466 0.8994 13 L 0.0603 0.0273 0.9123 14 P 0.0638 0.1122 0.8240 15 L 0.0105 0.8581 0.1314 16 E 0.0081 0.9184 0.0735 17 Y 0.0068 0.9340 0.0592 18 Q 0.0094 0.9374 0.0532 19 E 0.0114 0.9304 0.0582 20 K 0.0088 0.9097 0.0816 21 L 0.0313 0.8347 0.1339 22 K 0.0176 0.7626 0.2198 23 A 0.0364 0.5858 0.3778 24 I 0.0978 0.3186 0.5836 25 E 0.1081 0.1500 0.7419 26 P 0.0937 0.1720 0.7343 27 N 0.1201 0.1442 0.7357 28 D 0.0800 0.1156 0.8044 29 Y 0.0830 0.1142 0.8028 30 T 0.0611 0.1212 0.8177 31 G 0.0720 0.1014 0.8266 32 K 0.1636 0.1134 0.7230 33 V 0.2193 0.2037 0.5770 34 S 0.0910 0.2782 0.6308 35 E 0.0086 0.8959 0.0955 36 E 0.0061 0.9301 0.0638 37 I 0.0058 0.9403 0.0540 38 E 0.0057 0.9476 0.0467 39 D 0.0059 0.9431 0.0510 40 I 0.0063 0.9317 0.0620 41 I 0.0153 0.9025 0.0822 42 K 0.0190 0.8221 0.1589 43 K 0.0303 0.5673 0.4025 44 G 0.0380 0.2775 0.6844 45 E 0.0582 0.2223 0.7195 46 T 0.1281 0.2349 0.6370 47 Q 0.1575 0.2001 0.6424 48 T 0.1071 0.1150 0.7778 49 L 0.0441 0.0399 0.9159