# 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) # 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) # T0348.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0348.t2k.stride-ebghtl.rdb (weight 1.24869) # T0348.t2k.str2.rdb (weight 1.54758) # T0348.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 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 # # ============================================ # 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 # # ============================================ # Comments from T0348.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 155 # # ============================================ # Comments from T0348.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 155 # # ============================================ # Comments from T0348.t2k.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 155 # # ============================================ # Comments from T0348.t2k.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 155 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0444 0.0534 0.9022 2 D 0.0715 0.0987 0.8298 3 A 0.0096 0.7495 0.2409 4 K 0.0124 0.8126 0.1750 5 F 0.0108 0.8984 0.0908 6 L 0.0090 0.9356 0.0554 7 E 0.0100 0.9234 0.0666 8 I 0.0102 0.9134 0.0764 9 L 0.0154 0.8304 0.1542 10 V 0.0325 0.6385 0.3291 11 C 0.0594 0.1748 0.7657 12 P 0.0393 0.2514 0.7093 13 L 0.0516 0.3180 0.6304 14 C 0.0981 0.2319 0.6700 15 K 0.0948 0.1201 0.7850 16 G 0.1410 0.0548 0.8043 17 P 0.3011 0.0502 0.6487 18 L 0.5594 0.0383 0.4023 19 V 0.7085 0.0223 0.2692 20 F 0.6709 0.0264 0.3027 21 D 0.4000 0.0396 0.5604 22 K 0.0665 0.3050 0.6285 23 S 0.0451 0.2706 0.6842 24 K 0.0941 0.2306 0.6753 25 D 0.1397 0.1223 0.7380 26 E 0.6424 0.0491 0.3085 27 L 0.8046 0.0304 0.1650 28 I 0.7399 0.0346 0.2255 29 C 0.4510 0.0387 0.5103 30 K 0.0543 0.2963 0.6494 31 G 0.0240 0.3363 0.6397 32 D 0.0448 0.3158 0.6394 33 R 0.0794 0.1801 0.7405 34 L 0.2794 0.1321 0.5886 35 A 0.4382 0.0812 0.4805 36 F 0.4445 0.0246 0.5308 37 P 0.4067 0.0296 0.5636 38 I 0.3081 0.0942 0.5978 39 K 0.1822 0.1222 0.6957 40 D 0.0803 0.0684 0.8512 41 G 0.0525 0.0513 0.8962 42 I 0.2131 0.0430 0.7440 43 P 0.3496 0.0595 0.5909 44 M 0.4162 0.0947 0.4891 45 M 0.4681 0.0649 0.4671 46 L 0.2344 0.0557 0.7099 47 E 0.0330 0.6593 0.3077 48 S 0.0111 0.8205 0.1684 49 E 0.0148 0.8162 0.1690 50 A 0.0429 0.7208 0.2363 51 R 0.0636 0.6951 0.2412 52 E 0.0990 0.4919 0.4091 53 L 0.0855 0.2998 0.6147 54 A 0.0702 0.1249 0.8049 55 P 0.0227 0.4524 0.5249 56 E 0.0305 0.4548 0.5147 57 E 0.0645 0.4157 0.5198 58 E 0.1129 0.3710 0.5161 59 V 0.1092 0.1784 0.7124 60 K 0.0476 0.0868 0.8656