# This file is the result of combining several RDB files, specifically # T0386.t06.dssp-ebghstl.rdb (weight 1.53986) # T0386.t06.stride-ebghtl.rdb (weight 1.24869) # T0386.t06.str2.rdb (weight 1.54758) # T0386.t06.alpha.rdb (weight 0.659012) # T0386.t04.dssp-ebghstl.rdb (weight 1.53986) # T0386.t04.stride-ebghtl.rdb (weight 1.24869) # T0386.t04.str2.rdb (weight 1.54758) # T0386.t04.alpha.rdb (weight 0.659012) # T0386.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0386.t2k.stride-ebghtl.rdb (weight 1.24869) # T0386.t2k.str2.rdb (weight 1.54758) # T0386.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 T0386.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t04.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t04.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t04.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 8 # # ============================================ # Comments from T0386.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 8 # # ============================================ # Comments from T0386.t2k.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 8 # # ============================================ # Comments from T0386.t2k.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 8 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0573 0.0546 0.8881 2 P 0.0633 0.1467 0.7899 3 K 0.0643 0.2643 0.6714 4 A 0.0497 0.4315 0.5188 5 K 0.0602 0.4811 0.4587 6 A 0.0800 0.4748 0.4452 7 K 0.1043 0.4550 0.4407 8 T 0.1303 0.3386 0.5311 9 K 0.1215 0.2605 0.6180 10 N 0.1588 0.1443 0.6970 11 T 0.1761 0.1373 0.6866 12 E 0.3196 0.1248 0.5556 13 I 0.3580 0.1029 0.5391 14 I 0.3078 0.0586 0.6336 15 S 0.1858 0.0325 0.7816 16 P 0.1348 0.1422 0.7231 17 H 0.1482 0.1700 0.6818 18 H 0.1772 0.1994 0.6234 19 Y 0.3274 0.1576 0.5150 20 V 0.4656 0.0773 0.4571 21 Y 0.2359 0.0377 0.7264 22 P 0.0400 0.0903 0.8697 23 N 0.0396 0.0495 0.9109 24 T 0.1767 0.0927 0.7306 25 T 0.3011 0.1913 0.5076 26 T 0.4738 0.2472 0.2791 27 L 0.4851 0.2360 0.2789 28 K 0.4477 0.2092 0.3430 29 N 0.2935 0.2405 0.4660 30 K 0.1223 0.3317 0.5460 31 Y 0.0999 0.1601 0.7399 32 G 0.0942 0.0875 0.8183 33 I 0.1946 0.1112 0.6942 34 K 0.2804 0.1233 0.5963 35 N 0.1436 0.0831 0.7733 36 L 0.0056 0.8959 0.0985 37 N 0.0059 0.9258 0.0682 38 A 0.0059 0.9308 0.0633 39 F 0.0066 0.9356 0.0578 40 L 0.0085 0.9252 0.0663 41 E 0.0090 0.9026 0.0885 42 K 0.0123 0.8497 0.1380 43 C 0.0266 0.7615 0.2119 44 S 0.0228 0.6682 0.3090 45 H 0.0324 0.4870 0.4806 46 D 0.0316 0.4541 0.5144 47 T 0.0356 0.5358 0.4286 48 A 0.0061 0.9300 0.0640 49 K 0.0070 0.9414 0.0515 50 A 0.0072 0.9400 0.0528 51 M 0.0111 0.9305 0.0584 52 I 0.0157 0.9034 0.0809 53 N 0.0210 0.8282 0.1508 54 L 0.0576 0.6831 0.2593 55 R 0.1038 0.5096 0.3866 56 E 0.1016 0.3387 0.5597 57 E 0.0675 0.1338 0.7987 58 S 0.0705 0.0901 0.8393 59 L 0.0720 0.1136 0.8145 60 P 0.0395 0.2695 0.6909 61 E 0.0298 0.3297 0.6405 62 Y 0.0513 0.3013 0.6474 63 F 0.1614 0.1837 0.6549 64 D 0.1041 0.2460 0.6500 65 T 0.0086 0.8619 0.1295 66 A 0.0052 0.9277 0.0671 67 Y 0.0048 0.9347 0.0604 68 L 0.0060 0.9374 0.0566 69 C 0.0072 0.9298 0.0630 70 H 0.0080 0.9226 0.0694 71 I 0.0084 0.9050 0.0866 72 H 0.0133 0.8271 0.1597 73 Q 0.0184 0.5829 0.3987 74 Q 0.0271 0.4083 0.5646 75 L 0.0319 0.0860 0.8820