# This file is the result of combining several RDB files, specifically # T0379.t06.dssp-ebghstl.rdb (weight 1.53986) # T0379.t06.stride-ebghtl.rdb (weight 1.24869) # T0379.t06.str2.rdb (weight 1.54758) # T0379.t06.alpha.rdb (weight 0.659012) # T0379.t04.dssp-ebghstl.rdb (weight 1.53986) # T0379.t04.stride-ebghtl.rdb (weight 1.24869) # T0379.t04.str2.rdb (weight 1.54758) # T0379.t04.alpha.rdb (weight 0.659012) # T0379.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0379.t2k.stride-ebghtl.rdb (weight 1.24869) # T0379.t2k.str2.rdb (weight 1.54758) # T0379.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 T0379.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 7 # # ============================================ # Comments from T0379.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 7 # # ============================================ # Comments from T0379.t2k.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 7 # # ============================================ # Comments from T0379.t2k.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 7 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0699 0.0798 0.8503 2 L 0.0986 0.1225 0.7789 3 N 0.0973 0.0981 0.8046 4 R 0.0089 0.8276 0.1636 5 E 0.0064 0.9225 0.0711 6 E 0.0057 0.9402 0.0541 7 S 0.0057 0.9466 0.0477 8 I 0.0049 0.9535 0.0416 9 R 0.0048 0.9531 0.0421 10 R 0.0048 0.9472 0.0479 11 F 0.0052 0.9418 0.0530 12 K 0.0054 0.9349 0.0597 13 A 0.0058 0.9102 0.0841 14 I 0.0403 0.6535 0.3063 15 G 0.0446 0.1212 0.8342 16 V 0.0795 0.0781 0.8424 17 A 0.0986 0.0999 0.8015 18 D 0.1256 0.0718 0.8027 19 I 0.0113 0.7522 0.2365 20 E 0.0105 0.7672 0.2224 21 E 0.0129 0.7909 0.1962 22 M 0.0303 0.6068 0.3629 23 L 0.0714 0.3525 0.5761 24 D 0.0629 0.1577 0.7795 25 P 0.0089 0.8123 0.1788 26 Y 0.0076 0.8533 0.1392 27 L 0.0103 0.8772 0.1124 28 Q 0.0126 0.8808 0.1066 29 K 0.0142 0.8633 0.1226 30 G 0.0146 0.8166 0.1688 31 L 0.0173 0.8270 0.1557 32 F 0.0197 0.8451 0.1352 33 L 0.0135 0.8703 0.1162 34 D 0.0134 0.8551 0.1315 35 L 0.0242 0.7829 0.1930 36 E 0.0346 0.7115 0.2538 37 S 0.0479 0.3895 0.5625 38 G 0.0426 0.1236 0.8338 39 R 0.1061 0.0568 0.8371 40 K 0.2489 0.0375 0.7136 41 S 0.0781 0.0301 0.8918 42 E 0.0056 0.9166 0.0778 43 E 0.0049 0.9415 0.0535 44 E 0.0051 0.9435 0.0513 45 F 0.0050 0.9472 0.0479 46 R 0.0048 0.9490 0.0462 47 T 0.0050 0.9449 0.0501 48 E 0.0052 0.9373 0.0575 49 L 0.0056 0.9342 0.0602 50 S 0.0052 0.9303 0.0645 51 R 0.0061 0.8987 0.0952 52 Y 0.0092 0.8539 0.1369 53 I 0.0256 0.7182 0.2562 54 G 0.0278 0.3971 0.5751 55 K 0.0456 0.4239 0.5305 56 E 0.1032 0.3382 0.5586 57 L 0.1067 0.2286 0.6647 58 T 0.0711 0.1540 0.7749 59 Y 0.0055 0.9153 0.0792 60 Q 0.0048 0.9417 0.0535 61 Q 0.0051 0.9429 0.0520 62 V 0.0047 0.9511 0.0442 63 Y 0.0050 0.9530 0.0420 64 D 0.0051 0.9527 0.0422 65 A 0.0048 0.9523 0.0429 66 L 0.0053 0.9435 0.0511 67 L 0.0058 0.9248 0.0693 68 G 0.0071 0.8923 0.1006 69 F 0.0121 0.8218 0.1661 70 L 0.0380 0.5619 0.4001 71 E 0.0370 0.3160 0.6470 72 E 0.0392 0.0445 0.9164