# This file is the result of combining several RDB files, specifically # T0293.t06.dssp-ebghstl.rdb (weight 1.53986) # T0293.t06.stride-ebghtl.rdb (weight 1.24869) # T0293.t06.str2.rdb (weight 1.54758) # T0293.t06.alpha.rdb (weight 0.659012) # T0293.t04.dssp-ebghstl.rdb (weight 1.53986) # T0293.t04.stride-ebghtl.rdb (weight 1.24869) # T0293.t04.str2.rdb (weight 1.54758) # T0293.t04.alpha.rdb (weight 0.659012) # T0293.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0293.t2k.stride-ebghtl.rdb (weight 1.24869) # T0293.t2k.str2.rdb (weight 1.54758) # T0293.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 T0293.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.str2.rdb # ============================================ # TARGET T0293 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t06.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 5.9079 # # ============================================ # Comments from T0293.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 4.79834 # # ============================================ # Comments from T0293.t04.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 4.79834 # # ============================================ # Comments from T0293.t04.str2.rdb # ============================================ # TARGET T0293 # 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 T0293.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 4.79834 # # ============================================ # Comments from T0293.t04.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 4.79834 # # ============================================ # Comments from T0293.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 17 # # ============================================ # Comments from T0293.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 17 # # ============================================ # Comments from T0293.t2k.str2.rdb # ============================================ # TARGET T0293 # 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 T0293.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 17 # # ============================================ # Comments from T0293.t2k.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.5507 0.0122 0.4371 2 S 0.7360 0.0106 0.2534 3 L 0.7269 0.0160 0.2570 4 N 0.5240 0.0241 0.4519 5 F 0.1765 0.1158 0.7077 6 K 0.0711 0.1040 0.8249 7 D 0.0859 0.0758 0.8383 8 P 0.0056 0.8850 0.1093 9 E 0.0056 0.9192 0.0752 10 A 0.0054 0.9432 0.0514 11 V 0.0057 0.9512 0.0431 12 R 0.0052 0.9543 0.0405 13 A 0.0048 0.9537 0.0415 14 L 0.0048 0.9503 0.0448 15 T 0.0048 0.9481 0.0471 16 C 0.0048 0.9501 0.0451 17 T 0.0049 0.9455 0.0496 18 L 0.0053 0.9232 0.0715 19 L 0.0066 0.8962 0.0971 20 R 0.0055 0.8756 0.1189 21 E 0.0097 0.7617 0.2287 22 D 0.0148 0.6433 0.3419 23 F 0.0609 0.3702 0.5689 24 G 0.0520 0.0727 0.8753 25 L 0.1263 0.0281 0.8455 26 S 0.2495 0.0168 0.7338 27 I 0.4654 0.0141 0.5205 28 D 0.5402 0.0140 0.4458 29 I 0.3389 0.0173 0.6438 30 P 0.1142 0.0217 0.8641 31 L 0.0269 0.1880 0.7851 32 E 0.0208 0.1604 0.8188 33 R 0.1191 0.2058 0.6751 34 L 0.2868 0.0472 0.6660 35 I 0.1881 0.0253 0.7865 36 P 0.1616 0.0326 0.8059 37 T 0.1916 0.0499 0.7585 38 V 0.1537 0.0634 0.7829 39 P 0.1063 0.1795 0.7142 40 L 0.0939 0.1976 0.7085 41 R 0.3128 0.1383 0.5489 42 L 0.5063 0.1044 0.3892 43 N 0.5460 0.1040 0.3501 44 Y 0.7415 0.1011 0.1575 45 I 0.8046 0.0780 0.1174 46 H 0.8216 0.0646 0.1138 47 W 0.7969 0.0412 0.1618 48 V 0.5768 0.0464 0.3769 49 E 0.0965 0.0327 0.8708