# This file is the result of combining several RDB files, specifically # T0347.t04.dssp-ebghstl.rdb (weight 1.53986) # T0347.t04.stride-ebghtl.rdb (weight 1.24869) # T0347.t04.str2.rdb (weight 1.54758) # T0347.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 T0347.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.05 # # ============================================ # Comments from T0347.t04.stride-ebghtl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.05 # # ============================================ # Comments from T0347.t04.str2.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.05 # # ============================================ # Comments from T0347.t04.alpha.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.05 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0494 0.0225 0.9281 2 K 0.0343 0.4594 0.5064 3 D 0.0187 0.7169 0.2644 4 E 0.0169 0.7959 0.1871 5 F 0.0133 0.8918 0.0949 6 W 0.0094 0.9198 0.0708 7 S 0.0097 0.9237 0.0666 8 V 0.0103 0.9237 0.0660 9 M 0.0233 0.8612 0.1155 10 D 0.0184 0.7290 0.2527 11 H 0.0198 0.4509 0.5293 12 R 0.0525 0.1262 0.8212 13 N 0.0524 0.0510 0.8965 14 L 0.3173 0.0205 0.6622 15 I 0.5815 0.0144 0.4041 16 Y 0.6079 0.0138 0.3784 17 P 0.5134 0.0733 0.4133 18 F 0.4102 0.0813 0.5084 19 D 0.1608 0.0602 0.7790 20 A 0.0252 0.1912 0.7837 21 Q 0.0525 0.0688 0.8787 22 G 0.0635 0.0538 0.8827 23 L 0.1400 0.0163 0.8437 24 R 0.4048 0.0152 0.5800 25 R 0.2302 0.0273 0.7425 26 Q 0.1512 0.0464 0.8024 27 S 0.0300 0.6077 0.3622 28 G 0.0214 0.5160 0.4626 29 D 0.0317 0.5101 0.4582 30 I 0.0856 0.1262 0.7882 31 P 0.0840 0.1502 0.7657 32 K 0.0602 0.4487 0.4911 33 N 0.0748 0.4294 0.4957 34 I 0.0762 0.5954 0.3284 35 H 0.0659 0.4934 0.4407 36 D 0.0744 0.4362 0.4894 37 L 0.0670 0.4039 0.5292 38 E 0.0493 0.2993 0.6514 39 D 0.0560 0.1580 0.7860 40 D 0.0912 0.0533 0.8555 41 P 0.0110 0.6042 0.3848 42 F 0.0180 0.7126 0.2694 43 R 0.0157 0.8159 0.1684 44 S 0.0184 0.8879 0.0938 45 L 0.0121 0.9263 0.0616 46 A 0.0089 0.9457 0.0453 47 G 0.0068 0.9545 0.0386 48 A 0.0066 0.9554 0.0380 49 L 0.0122 0.9433 0.0445 50 R 0.0137 0.9221 0.0641 51 M 0.0185 0.8692 0.1123 52 A 0.0416 0.5015 0.4569 53 G 0.0331 0.0861 0.8808 54 G 0.0722 0.1027 0.8251 55 Y 0.1952 0.1279 0.6769 56 A 0.1943 0.1398 0.6659 57 K 0.1780 0.0828 0.7392 58 V 0.1759 0.0630 0.7611 59 I 0.2291 0.0498 0.7211 60 I 0.1864 0.0266 0.7870 61 P 0.1523 0.0804 0.7673 62 F 0.1049 0.3804 0.5147 63 S 0.0652 0.5568 0.3780 64 E 0.0750 0.6459 0.2791 65 F 0.0967 0.6434 0.2599 66 G 0.0844 0.6797 0.2359 67 W 0.0195 0.8730 0.1076 68 A 0.0081 0.9330 0.0588 69 D 0.0055 0.9518 0.0427 70 F 0.0056 0.9514 0.0430 71 L 0.0055 0.9413 0.0532 72 R 0.0070 0.8930 0.1000 73 R 0.0093 0.8162 0.1745 74 R 0.0195 0.6228 0.3578 75 I 0.0617 0.3129 0.6254 76 D 0.0617 0.1423 0.7960 77 R 0.0201 0.6504 0.3295 78 D 0.0160 0.6676 0.3164 79 L 0.0170 0.7111 0.2719 80 L 0.0391 0.4598 0.5011 81 S 0.0331 0.3744 0.5924 82 D 0.0132 0.4456 0.5411 83 S 0.0278 0.3829 0.5893 84 F 0.0206 0.6106 0.3688 85 D 0.0066 0.8862 0.1072 86 D 0.0048 0.9171 0.0780 87 A 0.0048 0.9345 0.0606 88 L 0.0047 0.9494 0.0459 89 A 0.0047 0.9531 0.0422 90 E 0.0048 0.9463 0.0489 91 A 0.0048 0.9460 0.0492 92 M 0.0048 0.9449 0.0503 93 K 0.0048 0.9262 0.0690 94 L 0.0051 0.8683 0.1266 95 A 0.0077 0.7665 0.2257 96 K 0.0157 0.5949 0.3894 97 S 0.0539 0.3455 0.6006 98 R 0.0069 0.6291 0.3640 99 E 0.0115 0.5546 0.4339 100 A 0.0213 0.6910 0.2877 101 R 0.0274 0.5515 0.4211 102 H 0.0394 0.3391 0.6215 103 L 0.1067 0.0607 0.8326 104 P 0.0619 0.1293 0.8088 105 G 0.1013 0.1050 0.7937 106 W 0.1818 0.1235 0.6947 107 C 0.1685 0.1135 0.7180 108 G 0.0984 0.0754 0.8262 109 V 0.0863 0.0640 0.8497 110 E 0.0759 0.0533 0.8708 111 E 0.0506 0.0413 0.9081