# This file is the result of combining several RDB files, specifically # T0303.t06.dssp-ebghstl.rdb (weight 1.53986) # T0303.t06.stride-ebghtl.rdb (weight 1.24869) # T0303.t06.str2.rdb (weight 1.54758) # T0303.t06.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 T0303.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.str2.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.0628 0.0849 0.8523 2 S 0.0965 0.2270 0.6765 3 L 0.0305 0.7314 0.2381 4 P 0.0137 0.8574 0.1288 5 D 0.0090 0.9219 0.0691 6 L 0.0048 0.9561 0.0392 7 A 0.0047 0.9586 0.0367 8 L 0.0047 0.9604 0.0349 9 S 0.0047 0.9599 0.0355 10 I 0.0047 0.9588 0.0365 11 N 0.0047 0.9587 0.0366 12 S 0.0048 0.9546 0.0406 13 A 0.0048 0.9533 0.0420 14 L 0.0048 0.9502 0.0450 15 K 0.0055 0.9339 0.0606 16 D 0.0065 0.8688 0.1247 17 V 0.0481 0.4948 0.4570 18 N 0.0338 0.0658 0.9004 19 L 0.0504 0.0163 0.9332 20 P 0.0650 0.0322 0.9028 21 Q 0.0905 0.0625 0.8470 22 A 0.0953 0.0471 0.8576 23 S 0.0700 0.0483 0.8817 24 E 0.0056 0.9082 0.0862 25 N 0.0067 0.9107 0.0826 26 L 0.0156 0.9087 0.0757 27 V 0.0308 0.8929 0.0763 28 M 0.0401 0.8782 0.0817 29 T 0.0488 0.8440 0.1072 30 W 0.0544 0.7941 0.1515 31 I 0.1026 0.6304 0.2670 32 G 0.0639 0.3537 0.5825 33 N 0.0391 0.4218 0.5391 34 G 0.0308 0.6299 0.3393 35 A 0.0095 0.8707 0.1198 36 D 0.0058 0.9227 0.0714 37 V 0.0082 0.9473 0.0444 38 L 0.0082 0.9512 0.0406 39 S 0.0068 0.9493 0.0439 40 Q 0.0064 0.9491 0.0445 41 R 0.0064 0.9417 0.0519 42 A 0.0070 0.9273 0.0657 43 V 0.0090 0.9104 0.0806 44 D 0.0096 0.9001 0.0903 45 W 0.0102 0.8743 0.1155 46 A 0.0127 0.8373 0.1500 47 C 0.0283 0.7949 0.1768 48 T 0.0337 0.7386 0.2277 49 Q 0.0387 0.7128 0.2485 50 A 0.0403 0.5993 0.3604 51 E 0.0510 0.3632 0.5858 52 K 0.0801 0.2801 0.6398 53 E 0.1083 0.1908 0.7009 54 L 0.1073 0.0740 0.8187 55 T 0.0529 0.0302 0.9168 56 E 0.0051 0.9346 0.0603 57 D 0.0048 0.9436 0.0516 58 E 0.0049 0.9485 0.0466 59 F 0.0047 0.9573 0.0380 60 K 0.0047 0.9566 0.0387 61 Y 0.0047 0.9509 0.0444 62 F 0.0050 0.9427 0.0523 63 K 0.0048 0.9534 0.0418 64 R 0.0050 0.9508 0.0443 65 Q 0.0057 0.9410 0.0533 66 F 0.0066 0.9374 0.0560 67 G 0.0059 0.9358 0.0583 68 F 0.0061 0.9310 0.0628 69 Y 0.0077 0.9203 0.0720 70 Y 0.0127 0.8880 0.0993 71 G 0.0133 0.8533 0.1334 72 E 0.0151 0.7990 0.1859 73 N 0.0328 0.7217 0.2456 74 L 0.0385 0.6787 0.2827 75 C 0.0629 0.5888 0.3484 76 N 0.0764 0.5475 0.3761 77 I 0.0948 0.4197 0.4855 78 S 0.0985 0.1870 0.7145 79 R 0.0530 0.1058 0.8412