# This file is the result of combining several RDB files, specifically # T0498.t04.dssp-ebghstl.rdb (weight 1.53986) # T0498.t04.stride-ebghtl.rdb (weight 1.24869) # T0498.t04.str2.rdb (weight 1.54758) # T0498.t04.alpha.rdb (weight 0.659012) # T0498.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0498.t2k.stride-ebghtl.rdb (weight 1.24869) # T0498.t2k.str2.rdb (weight 1.54758) # T0498.t2k.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 T0498.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0498 # Using neural net t04-2621-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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.stride-ebghtl.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.str2.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.alpha.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0498 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0498.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0498.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0498 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0498.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0498.t2k.str2.rdb # ============================================ # TARGET T0498 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0498.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0498.t2k.alpha.rdb # ============================================ # TARGET T0498 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0498.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1321 0.0183 0.8496 2 T 0.5192 0.0202 0.4606 3 Y 0.7717 0.0164 0.2119 4 K 0.8736 0.0114 0.1150 5 L 0.9106 0.0085 0.0810 6 I 0.9027 0.0144 0.0829 7 L 0.8628 0.0195 0.1177 8 N 0.6899 0.0334 0.2767 9 L 0.3282 0.0635 0.6084 10 K 0.2344 0.1042 0.6613 11 Q 0.3284 0.0926 0.5790 12 A 0.3504 0.1203 0.5293 13 K 0.3329 0.1751 0.4920 14 E 0.3789 0.2084 0.4127 15 E 0.4726 0.2183 0.3090 16 A 0.4824 0.2814 0.2363 17 I 0.4478 0.3455 0.2068 18 K 0.3163 0.4728 0.2109 19 E 0.2231 0.6070 0.1698 20 L 0.1812 0.6339 0.1849 21 V 0.1850 0.5763 0.2387 22 D 0.1128 0.4826 0.4047 23 A 0.0088 0.8716 0.1196 24 G 0.0075 0.9117 0.0809 25 T 0.0072 0.8982 0.0946 26 A 0.0048 0.9393 0.0559 27 E 0.0047 0.9497 0.0455 28 K 0.0048 0.9519 0.0432 29 Y 0.0047 0.9564 0.0389 30 I 0.0047 0.9562 0.0391 31 K 0.0047 0.9563 0.0390 32 L 0.0048 0.9517 0.0435 33 I 0.0049 0.9354 0.0598 34 A 0.0073 0.8932 0.0995 35 N 0.0119 0.7468 0.2413 36 A 0.0179 0.5505 0.4316 37 K 0.0522 0.2155 0.7323 38 T 0.0615 0.0476 0.8909 39 V 0.1870 0.0313 0.7818 40 E 0.3197 0.0436 0.6367 41 G 0.4635 0.0418 0.4947 42 V 0.6859 0.0329 0.2812 43 W 0.7629 0.0218 0.2152 44 T 0.6562 0.0206 0.3232 45 L 0.5301 0.0683 0.4016 46 K 0.2129 0.1836 0.6034 47 D 0.0895 0.2924 0.6181 48 E 0.1411 0.2372 0.6218 49 I 0.2315 0.1110 0.6574 50 K 0.3226 0.0824 0.5950 51 T 0.4945 0.0608 0.4447 52 F 0.6628 0.0379 0.2993 53 T 0.6947 0.0276 0.2777 54 V 0.4748 0.0399 0.4853 55 T 0.2558 0.0376 0.7065 56 E 0.0586 0.0309 0.9106