# This file is the result of combining several RDB files, specifically # T0311.t06.dssp-ebghstl.rdb (weight 1.53986) # T0311.t06.stride-ebghtl.rdb (weight 1.24869) # T0311.t06.str2.rdb (weight 1.54758) # T0311.t06.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 T0311.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.stride-ebghtl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.str2.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.alpha.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0636 0.0415 0.8948 2 K 0.1360 0.0720 0.7920 3 M 0.1460 0.1054 0.7485 4 A 0.1307 0.0905 0.7788 5 N 0.1060 0.0577 0.8363 6 H 0.0838 0.0189 0.8973 7 P 0.0903 0.0185 0.8912 8 R 0.0762 0.0270 0.8968 9 P 0.0149 0.7540 0.2311 10 G 0.0186 0.7984 0.1829 11 D 0.0289 0.8753 0.0958 12 I 0.0346 0.8822 0.0832 13 I 0.0165 0.9094 0.0741 14 Q 0.0092 0.9216 0.0691 15 E 0.0081 0.8961 0.0957 16 S 0.0091 0.8698 0.1211 17 L 0.0203 0.8773 0.1024 18 D 0.0070 0.8856 0.1074 19 E 0.0061 0.8405 0.1534 20 L 0.0465 0.4355 0.5180 21 N 0.0505 0.0327 0.9168 22 V 0.0822 0.0126 0.9052 23 S 0.1191 0.0210 0.8599 24 L 0.0052 0.9407 0.0541 25 R 0.0047 0.9561 0.0392 26 E 0.0047 0.9575 0.0378 27 F 0.0047 0.9604 0.0350 28 A 0.0047 0.9579 0.0374 29 R 0.0049 0.9444 0.0507 30 A 0.0055 0.8862 0.1082 31 M 0.0517 0.4578 0.4906 32 E 0.0406 0.0437 0.9158 33 I 0.0740 0.0168 0.9092 34 A 0.0627 0.0146 0.9227 35 P 0.0073 0.9067 0.0860 36 S 0.0059 0.9288 0.0653 37 T 0.0055 0.9408 0.0538 38 A 0.0052 0.9526 0.0422 39 S 0.0052 0.9522 0.0426 40 R 0.0058 0.9465 0.0477 41 L 0.0062 0.9419 0.0520 42 L 0.0101 0.8995 0.0904 43 T 0.0422 0.4927 0.4651 44 G 0.0317 0.2167 0.7516 45 K 0.0725 0.1956 0.7320 46 A 0.1113 0.1528 0.7359 47 A 0.1376 0.0886 0.7738 48 L 0.1527 0.0446 0.8027 49 T 0.0697 0.0388 0.8915 50 P 0.0049 0.9506 0.0445 51 E 0.0047 0.9591 0.0362 52 M 0.0049 0.9562 0.0389 53 A 0.0047 0.9600 0.0353 54 I 0.0047 0.9585 0.0368 55 K 0.0047 0.9539 0.0413 56 L 0.0050 0.9498 0.0451 57 S 0.0061 0.9447 0.0492 58 V 0.0064 0.9379 0.0557 59 V 0.0110 0.8842 0.1047 60 I 0.0506 0.5585 0.3910 61 G 0.0371 0.0702 0.8927 62 S 0.0640 0.0319 0.9041 63 S 0.0568 0.0289 0.9144 64 P 0.0057 0.9261 0.0682 65 Q 0.0049 0.9457 0.0494 66 M 0.0051 0.9489 0.0460 67 W 0.0063 0.9496 0.0441 68 L 0.0065 0.9404 0.0531 69 N 0.0062 0.9191 0.0747 70 L 0.0071 0.9087 0.0842 71 Q 0.0085 0.9093 0.0822 72 N 0.0083 0.8638 0.1279 73 A 0.0075 0.8706 0.1218 74 W 0.0320 0.7837 0.1843 75 S 0.0390 0.7130 0.2480 76 L 0.0080 0.9214 0.0707 77 A 0.0077 0.9387 0.0536 78 E 0.0106 0.9325 0.0569 79 A 0.0114 0.9230 0.0656 80 E 0.0149 0.9000 0.0851 81 K 0.0147 0.8333 0.1519 82 T 0.0209 0.7315 0.2476 83 V 0.0468 0.5729 0.3803 84 D 0.0778 0.3336 0.5887 85 V 0.0288 0.5944 0.3768 86 S 0.0436 0.6378 0.3186 87 R 0.0746 0.6397 0.2857 88 L 0.1094 0.5434 0.3472 89 R 0.1765 0.4679 0.3556 90 R 0.3405 0.3490 0.3105 91 L 0.3755 0.2814 0.3431 92 V 0.3520 0.2495 0.3986 93 T 0.2862 0.2233 0.4906 94 Q 0.2106 0.1532 0.6362 95 S 0.1256 0.0993 0.7751 96 T 0.0692 0.0229 0.9079 97 P 0.0434 0.0338 0.9228