# This file is the result of combining several RDB files, specifically # T0381.t06.dssp-ebghstl.rdb (weight 1.53986) # T0381.t06.stride-ebghtl.rdb (weight 1.24869) # T0381.t06.str2.rdb (weight 1.54758) # T0381.t06.alpha.rdb (weight 0.659012) # T0381.t04.dssp-ebghstl.rdb (weight 1.53986) # T0381.t04.stride-ebghtl.rdb (weight 1.24869) # T0381.t04.str2.rdb (weight 1.54758) # T0381.t04.alpha.rdb (weight 0.659012) # T0381.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0381.t2k.stride-ebghtl.rdb (weight 1.24869) # T0381.t2k.str2.rdb (weight 1.54758) # T0381.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 T0381.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 95 # # ============================================ # Comments from T0381.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 95 # # ============================================ # Comments from T0381.t2k.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 95 # # ============================================ # Comments from T0381.t2k.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 95 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1350 0.0290 0.8360 2 T 0.2340 0.0438 0.7223 3 A 0.1714 0.0796 0.7490 4 T 0.1634 0.0951 0.7415 5 E 0.1431 0.0840 0.7729 6 P 0.1473 0.1243 0.7285 7 T 0.0979 0.1910 0.7111 8 E 0.0579 0.3285 0.6136 9 K 0.0598 0.3553 0.5849 10 I 0.0580 0.3469 0.5951 11 L 0.0556 0.2813 0.6631 12 P 0.0524 0.2279 0.7198 13 S 0.0681 0.1713 0.7606 14 P 0.0085 0.7674 0.2241 15 D 0.0059 0.8360 0.1581 16 Y 0.0054 0.9163 0.0783 17 V 0.0060 0.9395 0.0545 18 Q 0.0054 0.9401 0.0545 19 S 0.0057 0.9396 0.0546 20 L 0.0049 0.9436 0.0515 21 A 0.0052 0.9364 0.0585 22 R 0.0071 0.8801 0.1128 23 G 0.0067 0.8276 0.1657 24 L 0.0176 0.8286 0.1538 25 A 0.0485 0.7434 0.2081 26 V 0.1477 0.7711 0.0812 27 I 0.1406 0.7775 0.0820 28 R 0.1475 0.7280 0.1245 29 C 0.1580 0.6432 0.1989 30 F 0.1115 0.3253 0.5632 31 D 0.0658 0.0839 0.8504 32 H 0.0181 0.2404 0.7415 33 R 0.0218 0.2203 0.7579 34 N 0.0606 0.1571 0.7823 35 Q 0.0670 0.1547 0.7783 36 R 0.1512 0.1048 0.7440 37 R 0.2020 0.0489 0.7490 38 T 0.1246 0.0424 0.8330 39 L 0.0049 0.9362 0.0589 40 S 0.0047 0.9531 0.0422 41 D 0.0048 0.9569 0.0384 42 V 0.0047 0.9593 0.0360 43 A 0.0047 0.9575 0.0377 44 R 0.0054 0.9423 0.0523 45 A 0.0069 0.8969 0.0962 46 T 0.0467 0.4875 0.4658 47 D 0.0383 0.0435 0.9182 48 L 0.0553 0.0135 0.9312 49 T 0.0526 0.0364 0.9110 50 R 0.0128 0.8718 0.1154 51 A 0.0048 0.9443 0.0509 52 T 0.0048 0.9553 0.0399 53 A 0.0047 0.9602 0.0351 54 R 0.0047 0.9603 0.0350 55 R 0.0047 0.9607 0.0346 56 F 0.0047 0.9609 0.0344 57 L 0.0047 0.9601 0.0352 58 L 0.0047 0.9603 0.0350 59 T 0.0047 0.9600 0.0353 60 L 0.0048 0.9584 0.0368 61 V 0.0052 0.9463 0.0484 62 E 0.0055 0.9089 0.0856 63 L 0.0411 0.4331 0.5258 64 G 0.0416 0.1219 0.8365 65 Y 0.2429 0.1188 0.6383 66 V 0.6632 0.0618 0.2749 67 A 0.6332 0.0567 0.3101 68 T 0.4040 0.0854 0.5106 69 D 0.1838 0.0386 0.7776 70 G 0.0627 0.0758 0.8614 71 S 0.0849 0.0878 0.8273 72 A 0.6288 0.0335 0.3377 73 F 0.7820 0.0211 0.1970 74 W 0.7925 0.0184 0.1892 75 L 0.6592 0.0385 0.3023 76 T 0.3165 0.0654 0.6181 77 P 0.0724 0.5841 0.3434 78 R 0.0580 0.6760 0.2660 79 V 0.0894 0.7932 0.1175 80 L 0.0676 0.8495 0.0829 81 E 0.0768 0.8245 0.0987 82 L 0.0359 0.8289 0.1352 83 G 0.0263 0.8264 0.1473 84 Y 0.0105 0.9110 0.0786 85 S 0.0143 0.8943 0.0914 86 Y 0.0156 0.8771 0.1073 87 L 0.0198 0.8212 0.1590 88 S 0.0209 0.6849 0.2942 89 S 0.0385 0.4081 0.5534 90 L 0.0594 0.0698 0.8708 91 S 0.0508 0.0252 0.9240