# This file is the result of combining several RDB files, specifically # T0344.t04.dssp-ebghstl.rdb (weight 1.53986) # T0344.t04.stride-ebghtl.rdb (weight 1.24869) # T0344.t04.str2.rdb (weight 1.54758) # T0344.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 T0344.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.3857 0.0240 0.5903 2 I 0.6925 0.0290 0.2785 3 I 0.6795 0.0471 0.2735 4 G 0.5356 0.0311 0.4333 5 L 0.3947 0.0315 0.5737 6 P 0.4028 0.0501 0.5472 7 R 0.4684 0.0807 0.4509 8 Y 0.7229 0.0319 0.2452 9 M 0.8079 0.0111 0.1810 10 E 0.8732 0.0068 0.1200 11 V 0.8808 0.0051 0.1140 12 N 0.8849 0.0044 0.1108 13 I 0.7422 0.0103 0.2475 14 K 0.4795 0.0273 0.4932 15 D 0.0797 0.0433 0.8769 16 G 0.0672 0.0363 0.8965 17 K 0.5731 0.0181 0.4088 18 I 0.8406 0.0067 0.1527 19 I 0.7360 0.0235 0.2404 20 G 0.5289 0.0344 0.4368 21 R 0.4548 0.0435 0.5017 22 S 0.4786 0.0281 0.4933 23 L 0.3845 0.0231 0.5924 24 D 0.2074 0.0114 0.7812 25 P 0.0248 0.2734 0.7018 26 R 0.0301 0.2398 0.7301 27 E 0.1015 0.2221 0.6764 28 G 0.1433 0.0873 0.7694 29 G 0.2659 0.0621 0.6720 30 L 0.5462 0.0494 0.4045 31 Y 0.5759 0.0435 0.3806 32 G 0.5753 0.0236 0.4010 33 S 0.7424 0.0177 0.2399 34 A 0.8325 0.0142 0.1533 35 E 0.8671 0.0118 0.1212 36 V 0.8515 0.0104 0.1382 37 S 0.7517 0.0138 0.2345 38 V 0.3998 0.0167 0.5835 39 P 0.1875 0.0464 0.7661 40 E 0.0702 0.0721 0.8578 41 G 0.1763 0.0414 0.7823 42 V 0.5433 0.0077 0.4490 43 K 0.8056 0.0108 0.1836 44 W 0.8786 0.0082 0.1131 45 E 0.8600 0.0128 0.1272 46 I 0.7981 0.0161 0.1858 47 Y 0.4631 0.0126 0.5243 48 P 0.1589 0.0521 0.7890 49 N 0.1085 0.0688 0.8227 50 P 0.0177 0.6061 0.3763 51 V 0.0330 0.6779 0.2891 52 A 0.0916 0.6987 0.2096 53 R 0.1742 0.6415 0.1844 54 R 0.2886 0.5154 0.1960 55 F 0.4372 0.3787 0.1842 56 M 0.5537 0.3137 0.1326 57 I 0.6254 0.2806 0.0940 58 F 0.6322 0.2734 0.0944 59 E 0.6429 0.2613 0.0958 60 I 0.6063 0.2426 0.1512 61 F 0.4791 0.1700 0.3509 62 S 0.2733 0.1208 0.6059 63 K 0.1277 0.1103 0.7620 64 R 0.0661 0.0443 0.8896