# This file is the result of combining several RDB files, specifically # T0348.t04.dssp-ebghstl.rdb (weight 1.53986) # T0348.t04.stride-ebghtl.rdb (weight 1.24869) # T0348.t04.str2.rdb (weight 1.54758) # T0348.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 T0348.t04.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.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 16.8038 # # ============================================ # Comments from T0348.t04.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8038 # # ============================================ # Comments from T0348.t04.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8038 # # ============================================ # Comments from T0348.t04.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 16.8038 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0575 0.0381 0.9044 2 D 0.0703 0.0427 0.8870 3 A 0.0076 0.8105 0.1819 4 K 0.0079 0.8496 0.1425 5 F 0.0091 0.8901 0.1008 6 L 0.0189 0.8619 0.1192 7 E 0.0304 0.8519 0.1177 8 I 0.0571 0.8160 0.1269 9 L 0.0986 0.6925 0.2089 10 V 0.1620 0.3921 0.4459 11 C 0.1479 0.0980 0.7542 12 P 0.0700 0.2229 0.7070 13 L 0.0757 0.2004 0.7239 14 C 0.1485 0.1185 0.7331 15 K 0.1060 0.0853 0.8087 16 G 0.1453 0.0522 0.8025 17 P 0.3033 0.0809 0.6159 18 L 0.4865 0.0619 0.4516 19 V 0.7249 0.0368 0.2383 20 F 0.7445 0.0322 0.2234 21 D 0.5177 0.0281 0.4542 22 K 0.2205 0.2136 0.5659 23 S 0.1803 0.1721 0.6477 24 K 0.1054 0.1473 0.7473 25 D 0.1173 0.0970 0.7857 26 E 0.6063 0.0725 0.3212 27 L 0.7668 0.0387 0.1945 28 I 0.7411 0.0380 0.2209 29 C 0.5149 0.0341 0.4511 30 K 0.1272 0.1633 0.7094 31 G 0.0931 0.1431 0.7638 32 D 0.1682 0.1816 0.6502 33 R 0.2038 0.2076 0.5887 34 L 0.3967 0.1209 0.4824 35 A 0.5855 0.0769 0.3376 36 F 0.5426 0.0342 0.4232 37 P 0.5011 0.0327 0.4662 38 I 0.3405 0.1483 0.5111 39 K 0.2223 0.1848 0.5929 40 D 0.0689 0.1442 0.7869 41 G 0.0829 0.0739 0.8432 42 I 0.2403 0.0390 0.7206 43 P 0.5291 0.0570 0.4139 44 M 0.5998 0.1188 0.2815 45 M 0.5405 0.1144 0.3450 46 L 0.3543 0.1276 0.5182 47 E 0.1132 0.5499 0.3368 48 S 0.0376 0.7400 0.2224 49 E 0.0245 0.7625 0.2130 50 A 0.0466 0.7082 0.2451 51 R 0.0532 0.6295 0.3172 52 E 0.0653 0.4957 0.4390 53 L 0.0838 0.2149 0.7013 54 A 0.0636 0.0298 0.9066 55 P 0.0140 0.5156 0.4704 56 E 0.0164 0.5922 0.3914 57 E 0.0367 0.5889 0.3744 58 E 0.0869 0.3369 0.5762 59 V 0.0856 0.1090 0.8054 60 K 0.0462 0.0459 0.9079