# This file is the result of combining several RDB files, specifically # T0358.t04.dssp-ebghstl.rdb (weight 1.53986) # T0358.t04.stride-ebghtl.rdb (weight 1.24869) # T0358.t04.str2.rdb (weight 1.54758) # T0358.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 T0358.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.10017 # # ============================================ # Comments from T0358.t04.stride-ebghtl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.10017 # # ============================================ # Comments from T0358.t04.str2.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.10017 # # ============================================ # Comments from T0358.t04.alpha.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.10017 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0999 0.0433 0.8568 2 T 0.1687 0.0558 0.7755 3 Q 0.2331 0.1227 0.6442 4 S 0.3793 0.1228 0.4979 5 V 0.5288 0.0732 0.3981 6 L 0.5269 0.0336 0.4394 7 L 0.2245 0.0170 0.7584 8 P 0.1167 0.0182 0.8651 9 P 0.0616 0.0794 0.8590 10 G 0.0673 0.0569 0.8758 11 P 0.1073 0.1217 0.7710 12 F 0.1632 0.1539 0.6829 13 T 0.1619 0.2265 0.6115 14 R 0.0176 0.8856 0.0969 15 R 0.0231 0.8829 0.0940 16 Q 0.0354 0.8674 0.0973 17 A 0.0599 0.8572 0.0829 18 Q 0.1114 0.8007 0.0878 19 A 0.1821 0.7325 0.0854 20 V 0.2340 0.6646 0.1015 21 T 0.2949 0.5570 0.1481 22 T 0.3172 0.4527 0.2301 23 T 0.3326 0.2594 0.4079 24 Y 0.4288 0.1482 0.4230 25 S 0.3910 0.1262 0.4828 26 N 0.3879 0.0645 0.5477 27 I 0.5626 0.0297 0.4077 28 T 0.7477 0.0209 0.2313 29 L 0.7346 0.0354 0.2300 30 E 0.5334 0.0569 0.4097 31 D 0.2303 0.0466 0.7232 32 D 0.0984 0.0728 0.8289 33 Q 0.0703 0.1039 0.8258 34 G 0.0912 0.1198 0.7891 35 S 0.1880 0.1134 0.6987 36 H 0.4856 0.0590 0.4554 37 F 0.7738 0.0203 0.2059 38 R 0.8726 0.0119 0.1155 39 L 0.9199 0.0060 0.0741 40 V 0.9202 0.0076 0.0722 41 V 0.9162 0.0060 0.0778 42 R 0.8708 0.0113 0.1179 43 D 0.4105 0.0209 0.5686 44 T 0.0591 0.1216 0.8193 45 E 0.0510 0.0325 0.9165 46 G 0.0715 0.0335 0.8950 47 R 0.3781 0.0204 0.6015 48 M 0.8707 0.0040 0.1253 49 V 0.8946 0.0084 0.0970 50 W 0.9072 0.0073 0.0855 51 R 0.8651 0.0127 0.1221 52 A 0.7412 0.0284 0.2305 53 W 0.3754 0.0777 0.5469 54 N 0.2109 0.0506 0.7385 55 F 0.1619 0.0683 0.7698 56 E 0.1008 0.0711 0.8281 57 P 0.0551 0.1944 0.7505 58 D 0.0456 0.1960 0.7584 59 A 0.0456 0.4262 0.5282 60 G 0.0252 0.5212 0.4536 61 E 0.0242 0.6889 0.2868 62 G 0.0339 0.7588 0.2072 63 L 0.0345 0.8086 0.1568 64 N 0.0310 0.8279 0.1411 65 R 0.0170 0.9008 0.0822 66 Y 0.0167 0.9094 0.0739 67 I 0.0249 0.8925 0.0825 68 R 0.0294 0.8411 0.1294 69 T 0.0292 0.7589 0.2119 70 S 0.0466 0.4185 0.5349 71 G 0.0554 0.1464 0.7983 72 I 0.2047 0.1064 0.6889 73 R 0.2786 0.1052 0.6163 74 T 0.2064 0.1855 0.6080 75 D 0.1411 0.1617 0.6971 76 T 0.1568 0.1876 0.6556 77 A 0.1836 0.1153 0.7010 78 T 0.1153 0.0633 0.8214 79 R 0.0590 0.0415 0.8995