# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0551 0.0196 0.9253 2 P 0.0665 0.0692 0.8643 3 K 0.0579 0.2771 0.6651 4 A 0.0561 0.3771 0.5668 5 K 0.0596 0.4131 0.5273 6 A 0.0765 0.3799 0.5436 7 K 0.0936 0.2900 0.6164 8 T 0.1621 0.1708 0.6671 9 K 0.1518 0.1586 0.6896 10 N 0.1988 0.0942 0.7069 11 T 0.3080 0.1095 0.5826 12 E 0.5211 0.0952 0.3837 13 I 0.6178 0.0594 0.3229 14 I 0.4859 0.0506 0.4635 15 S 0.2269 0.0358 0.7373 16 P 0.1033 0.1346 0.7621 17 H 0.1501 0.1681 0.6818 18 H 0.1966 0.1695 0.6339 19 Y 0.3116 0.0702 0.6182 20 V 0.4959 0.0524 0.4517 21 Y 0.2199 0.0333 0.7469 22 P 0.0508 0.1002 0.8490 23 N 0.0526 0.0684 0.8790 24 T 0.1342 0.1649 0.7009 25 T 0.1930 0.3109 0.4961 26 T 0.3398 0.3929 0.2673 27 L 0.3301 0.4273 0.2426 28 K 0.2587 0.4658 0.2755 29 N 0.1788 0.4284 0.3928 30 K 0.0809 0.5533 0.3658 31 Y 0.0862 0.3420 0.5718 32 G 0.0758 0.2393 0.6849 33 I 0.1201 0.2968 0.5831 34 K 0.1532 0.2897 0.5571 35 N 0.1419 0.1699 0.6882 36 L 0.0069 0.9195 0.0736 37 N 0.0054 0.9418 0.0528 38 A 0.0058 0.9412 0.0530 39 F 0.0066 0.9365 0.0569 40 L 0.0073 0.9333 0.0594 41 E 0.0080 0.9109 0.0810 42 K 0.0111 0.8550 0.1339 43 C 0.0253 0.6755 0.2993 44 S 0.0328 0.5204 0.4468 45 H 0.0379 0.5068 0.4553 46 D 0.0298 0.6420 0.3282 47 T 0.0161 0.7462 0.2376 48 A 0.0149 0.8612 0.1239 49 K 0.0246 0.8688 0.1066 50 A 0.0530 0.8308 0.1162 51 M 0.1082 0.7683 0.1235 52 I 0.1448 0.6947 0.1605 53 N 0.1598 0.5833 0.2569 54 L 0.0917 0.5709 0.3374 55 R 0.0890 0.4773 0.4337 56 E 0.0922 0.3885 0.5193 57 E 0.0891 0.1906 0.7203 58 S 0.0765 0.1696 0.7539 59 L 0.0663 0.0887 0.8450 60 P 0.0466 0.4064 0.5469 61 E 0.0254 0.5035 0.4711 62 Y 0.0466 0.5349 0.4185 63 F 0.1087 0.3340 0.5573 64 D 0.0584 0.4261 0.5155 65 T 0.0522 0.7706 0.1772 66 A 0.0437 0.8702 0.0860 67 Y 0.0430 0.8858 0.0711 68 L 0.0355 0.8974 0.0671 69 C 0.0218 0.9197 0.0585 70 H 0.0191 0.9173 0.0636 71 I 0.0162 0.9034 0.0804 72 H 0.0187 0.8793 0.1020 73 Q 0.0180 0.8196 0.1624 74 Q 0.0172 0.6703 0.3126 75 L 0.0278 0.1762 0.7960