# This file is the result of combining several RDB files, specifically # T0348.t06.dssp-ebghstl.rdb (weight 1.53986) # T0348.t06.stride-ebghtl.rdb (weight 1.24869) # T0348.t06.str2.rdb (weight 1.54758) # T0348.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 T0348.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8385 # # ============================================ # Comments from T0348.t06.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8385 # # ============================================ # Comments from T0348.t06.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8385 # # ============================================ # Comments from T0348.t06.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8385 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0478 0.0325 0.9197 2 D 0.0699 0.0306 0.8995 3 A 0.0067 0.8192 0.1741 4 K 0.0097 0.8062 0.1841 5 F 0.0107 0.8660 0.1232 6 L 0.0222 0.8282 0.1496 7 E 0.0371 0.8354 0.1275 8 I 0.0537 0.8238 0.1224 9 L 0.0976 0.7098 0.1926 10 V 0.1561 0.4522 0.3917 11 C 0.1355 0.1038 0.7607 12 P 0.0778 0.1851 0.7371 13 L 0.1086 0.1600 0.7314 14 C 0.1528 0.0942 0.7531 15 K 0.1005 0.0803 0.8192 16 G 0.1368 0.0430 0.8203 17 P 0.3083 0.0673 0.6243 18 L 0.5480 0.0453 0.4067 19 V 0.8028 0.0248 0.1724 20 F 0.7972 0.0250 0.1778 21 D 0.5666 0.0289 0.4045 22 K 0.2474 0.2005 0.5521 23 S 0.1950 0.1689 0.6361 24 K 0.1034 0.1603 0.7363 25 D 0.1103 0.1183 0.7714 26 E 0.5340 0.0870 0.3790 27 L 0.7281 0.0545 0.2174 28 I 0.7123 0.0442 0.2435 29 C 0.4320 0.0377 0.5303 30 K 0.0817 0.1947 0.7236 31 G 0.0542 0.1690 0.7768 32 D 0.1119 0.2091 0.6790 33 R 0.1786 0.1911 0.6303 34 L 0.4050 0.1130 0.4820 35 A 0.5446 0.0784 0.3770 36 F 0.5568 0.0322 0.4110 37 P 0.5065 0.0355 0.4579 38 I 0.3048 0.1461 0.5491 39 K 0.2057 0.1873 0.6070 40 D 0.0702 0.1432 0.7866 41 G 0.0710 0.0890 0.8400 42 I 0.2348 0.0708 0.6944 43 P 0.4682 0.1015 0.4303 44 M 0.4909 0.1596 0.3495 45 M 0.4401 0.1561 0.4038 46 L 0.2722 0.1743 0.5534 47 E 0.0650 0.6498 0.2852 48 S 0.0282 0.7650 0.2068 49 E 0.0254 0.7591 0.2155 50 A 0.0541 0.6854 0.2605 51 R 0.0687 0.6226 0.3087 52 E 0.0915 0.4853 0.4231 53 L 0.0981 0.2292 0.6727 54 A 0.0637 0.0316 0.9047 55 P 0.0167 0.4306 0.5527 56 E 0.0200 0.5229 0.4571 57 E 0.0423 0.5333 0.4244 58 E 0.1025 0.2949 0.6026 59 V 0.0985 0.1110 0.7905 60 K 0.0461 0.0326 0.9213