# This file is the result of combining several RDB files, specifically # T0404.t04.dssp-ebghstl.rdb (weight 1.53986) # T0404.t04.stride-ebghtl.rdb (weight 1.24869) # T0404.t04.str2.rdb (weight 1.54758) # T0404.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 T0404.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0404 # Using neural net t04-2621-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 T0404.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 82.5734 # # ============================================ # Comments from T0404.t04.stride-ebghtl.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5734 # # ============================================ # Comments from T0404.t04.str2.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5734 # # ============================================ # Comments from T0404.t04.alpha.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5734 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0546 0.0711 0.8743 2 S 0.0651 0.1096 0.8253 3 K 0.0528 0.2614 0.6858 4 R 0.0624 0.2211 0.7165 5 A 0.1974 0.1175 0.6851 6 N 0.3127 0.0918 0.5956 7 K 0.7842 0.0220 0.1938 8 L 0.8815 0.0102 0.1082 9 V 0.9181 0.0123 0.0695 10 I 0.9146 0.0113 0.0741 11 V 0.8702 0.0261 0.1037 12 T 0.6567 0.0411 0.3022 13 E 0.1985 0.0778 0.7237 14 K 0.0206 0.7659 0.2134 15 V 0.0154 0.8139 0.1707 16 L 0.0102 0.8562 0.1336 17 L 0.0061 0.9270 0.0669 18 K 0.0053 0.9470 0.0477 19 K 0.0047 0.9571 0.0382 20 V 0.0047 0.9586 0.0367 21 A 0.0047 0.9609 0.0344 22 K 0.0047 0.9612 0.0342 23 I 0.0047 0.9612 0.0341 24 I 0.0047 0.9605 0.0348 25 E 0.0049 0.9537 0.0414 26 E 0.0059 0.9314 0.0627 27 A 0.0434 0.5259 0.4307 28 G 0.0399 0.0210 0.9391 29 A 0.0772 0.0107 0.9121 30 T 0.1787 0.0449 0.7765 31 G 0.5227 0.0248 0.4525 32 Y 0.7237 0.0087 0.2676 33 T 0.8685 0.0060 0.1255 34 V 0.8704 0.0134 0.1163 35 V 0.7707 0.0269 0.2024 36 D 0.6432 0.0253 0.3315 37 T 0.4741 0.0517 0.4742 38 G 0.3343 0.0536 0.6121 39 G 0.2999 0.0426 0.6575 40 K 0.3391 0.0577 0.6033 41 G 0.2730 0.0466 0.6804 42 S 0.1907 0.0784 0.7309 43 R 0.1494 0.0930 0.7576 44 N 0.1709 0.0748 0.7543 45 V 0.4491 0.0523 0.4986 46 R 0.5657 0.0441 0.3902 47 S 0.4890 0.0617 0.4493 48 T 0.2796 0.0706 0.6497 49 G 0.1373 0.0396 0.8231 50 K 0.1735 0.0261 0.8004 51 P 0.2439 0.0889 0.6672 52 N 0.3437 0.1007 0.5556 53 T 0.4103 0.0977 0.4920 54 S 0.3803 0.0977 0.5219 55 D 0.3094 0.0807 0.6099 56 T 0.2021 0.1308 0.6672 57 D 0.1599 0.1173 0.7228 58 S 0.0745 0.1426 0.7829 59 N 0.2210 0.0600 0.7190 60 V 0.7395 0.0052 0.2553 61 K 0.8935 0.0038 0.1027 62 F 0.9274 0.0031 0.0695 63 E 0.9292 0.0035 0.0674 64 V 0.9258 0.0033 0.0709 65 L 0.8717 0.0047 0.1235 66 T 0.5693 0.0087 0.4220 67 E 0.1425 0.0287 0.8287 68 N 0.0743 0.0856 0.8401 69 R 0.0076 0.8376 0.1548 70 E 0.0055 0.9253 0.0691 71 M 0.0052 0.9418 0.0530 72 A 0.0050 0.9557 0.0393 73 E 0.0047 0.9589 0.0364 74 K 0.0047 0.9588 0.0365 75 I 0.0047 0.9598 0.0355 76 A 0.0047 0.9610 0.0343 77 D 0.0046 0.9611 0.0343 78 Q 0.0047 0.9596 0.0358 79 V 0.0047 0.9547 0.0406 80 A 0.0049 0.9450 0.0502 81 I 0.0057 0.9240 0.0704 82 K 0.0105 0.8477 0.1418 83 F 0.0389 0.6773 0.2838 84 F 0.1167 0.3834 0.4999 85 T 0.1692 0.1351 0.6957 86 D 0.0689 0.0674 0.8637 87 Y 0.0795 0.0712 0.8494 88 A 0.0938 0.0470 0.8592 89 G 0.2987 0.0177 0.6835 90 I 0.7525 0.0044 0.2432 91 I 0.9203 0.0036 0.0761 92 Y 0.9248 0.0036 0.0716 93 I 0.9172 0.0045 0.0782 94 C 0.8194 0.0093 0.1713 95 E 0.6488 0.0073 0.3440 96 A 0.5217 0.0211 0.4572 97 E 0.6083 0.0251 0.3665 98 V 0.8143 0.0125 0.1731 99 L 0.8608 0.0074 0.1318 100 Y 0.8634 0.0091 0.1275 101 G 0.7221 0.0203 0.2576 102 R 0.4792 0.0530 0.4678 103 T 0.3946 0.0343 0.5711 104 F 0.2315 0.0413 0.7273 105 C 0.2262 0.0454 0.7284 106 G 0.1256 0.0381 0.8363 107 P 0.0544 0.1464 0.7992 108 D 0.0427 0.2088 0.7485 109 G 0.0536 0.1872 0.7592 110 C 0.0682 0.0610 0.8708