# This file is the result of combining several RDB files, specifically # T0342.t04.dssp-ebghstl.rdb (weight 1.53986) # T0342.t04.stride-ebghtl.rdb (weight 1.24869) # T0342.t04.str2.rdb (weight 1.54758) # T0342.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 T0342.t04.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.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 3.73689 # # ============================================ # Comments from T0342.t04.stride-ebghtl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.73689 # # ============================================ # Comments from T0342.t04.str2.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.73689 # # ============================================ # Comments from T0342.t04.alpha.rdb # ============================================ # TARGET T0342 # 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 T0342.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 3.73689 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.1142 0.0117 0.8741 2 K 0.6246 0.0076 0.3678 3 I 0.8983 0.0041 0.0976 4 I 0.9248 0.0043 0.0709 5 C 0.9046 0.0076 0.0878 6 M 0.7239 0.0420 0.2341 7 G 0.3637 0.0283 0.6080 8 A 0.1997 0.2790 0.5213 9 K 0.0816 0.5083 0.4102 10 E 0.0736 0.4839 0.4425 11 N 0.0696 0.1398 0.7906 12 G 0.0491 0.0473 0.9036 13 L 0.0796 0.0237 0.8967 14 P 0.0828 0.1051 0.8121 15 L 0.0085 0.8904 0.1011 16 E 0.0073 0.9234 0.0694 17 Y 0.0065 0.9352 0.0583 18 Q 0.0077 0.9436 0.0487 19 E 0.0077 0.9342 0.0581 20 K 0.0070 0.9171 0.0759 21 L 0.0129 0.8717 0.1154 22 K 0.0172 0.7719 0.2109 23 A 0.0339 0.5518 0.4143 24 I 0.1170 0.2124 0.6705 25 E 0.0946 0.0569 0.8485 26 P 0.0636 0.1726 0.7637 27 N 0.0805 0.1247 0.7949 28 D 0.0987 0.1810 0.7203 29 Y 0.1283 0.1388 0.7329 30 T 0.1346 0.0948 0.7706 31 G 0.1100 0.0512 0.8389 32 K 0.1863 0.0551 0.7586 33 V 0.1268 0.0432 0.8300 34 S 0.0580 0.0836 0.8584 35 E 0.0080 0.8876 0.1044 36 E 0.0091 0.8983 0.0926 37 I 0.0050 0.9441 0.0509 38 E 0.0050 0.9520 0.0430 39 D 0.0050 0.9525 0.0425 40 I 0.0049 0.9467 0.0484 41 I 0.0079 0.9268 0.0654 42 K 0.0120 0.8559 0.1321 43 K 0.0212 0.6178 0.3610 44 G 0.0279 0.2172 0.7549 45 E 0.0531 0.2041 0.7428 46 T 0.1082 0.2358 0.6561 47 Q 0.1164 0.1833 0.7003 48 T 0.0885 0.0592 0.8523 49 L 0.0530 0.0320 0.9150