# This file is the result of combining several RDB files, specifically # T0382.t06.dssp-ebghstl.rdb (weight 1.53986) # T0382.t06.stride-ebghtl.rdb (weight 1.24869) # T0382.t06.str2.rdb (weight 1.54758) # T0382.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 T0382.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.stride-ebghtl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.str2.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.alpha.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0685 0.0396 0.8919 2 S 0.1192 0.0801 0.8007 3 K 0.1467 0.1285 0.7248 4 L 0.1703 0.1079 0.7218 5 D 0.1768 0.0821 0.7411 6 L 0.0676 0.4975 0.4350 7 H 0.0709 0.4658 0.4633 8 Q 0.1584 0.3281 0.5136 9 M 0.2160 0.0539 0.7301 10 T 0.1911 0.0418 0.7671 11 T 0.0137 0.8914 0.0950 12 Q 0.0049 0.9420 0.0531 13 D 0.0048 0.9470 0.0482 14 L 0.0047 0.9554 0.0399 15 V 0.0047 0.9589 0.0364 16 A 0.0047 0.9602 0.0352 17 L 0.0047 0.9592 0.0361 18 F 0.0047 0.9582 0.0371 19 A 0.0047 0.9574 0.0378 20 K 0.0047 0.9562 0.0391 21 V 0.0049 0.9443 0.0508 22 T 0.0056 0.9277 0.0667 23 V 0.0065 0.8987 0.0947 24 E 0.0085 0.8501 0.1414 25 Q 0.0077 0.8643 0.1280 26 D 0.0083 0.8912 0.1005 27 D 0.0077 0.8757 0.1167 28 A 0.0106 0.8778 0.1116 29 L 0.0235 0.8038 0.1727 30 L 0.0251 0.6967 0.2782 31 G 0.0178 0.7050 0.2772 32 N 0.0187 0.6940 0.2873 33 Q 0.0222 0.7380 0.2398 34 I 0.0149 0.8413 0.1438 35 S 0.0106 0.8749 0.1144 36 R 0.0088 0.9061 0.0851 37 F 0.0096 0.9133 0.0770 38 N 0.0099 0.9010 0.0891 39 R 0.0067 0.9160 0.0773 40 L 0.0056 0.9190 0.0753 41 F 0.0058 0.9340 0.0602 42 G 0.0055 0.9362 0.0583 43 V 0.0057 0.9465 0.0477 44 M 0.0048 0.9546 0.0406 45 A 0.0047 0.9563 0.0390 46 E 0.0047 0.9541 0.0411 47 I 0.0049 0.9474 0.0477 48 A 0.0048 0.9491 0.0460 49 D 0.0048 0.9402 0.0550 50 E 0.0051 0.9290 0.0659 51 L 0.0072 0.8994 0.0934 52 K 0.0100 0.7889 0.2011 53 A 0.0166 0.5965 0.3869 54 R 0.0550 0.1818 0.7631 55 D 0.0409 0.1441 0.8151 56 G 0.0281 0.1975 0.7744 57 D 0.0525 0.3662 0.5813 58 Q 0.0330 0.7404 0.2267 59 R 0.0201 0.8737 0.1062 60 T 0.0179 0.9039 0.0782 61 A 0.0223 0.8983 0.0794 62 L 0.0189 0.8848 0.0962 63 L 0.0161 0.8848 0.0991 64 S 0.0183 0.8592 0.1225 65 L 0.0190 0.7995 0.1815 66 F 0.0506 0.6116 0.3378 67 E 0.0636 0.3700 0.5664 68 Y 0.0813 0.0602 0.8584 69 P 0.0156 0.2148 0.7696 70 N 0.0404 0.2448 0.7148 71 M 0.0591 0.6161 0.3248 72 Q 0.0684 0.7939 0.1377 73 V 0.0884 0.8241 0.0875 74 R 0.0444 0.8860 0.0696 75 L 0.0145 0.9374 0.0481 76 Q 0.0106 0.9359 0.0536 77 A 0.0095 0.9373 0.0533 78 A 0.0181 0.9237 0.0582 79 K 0.0209 0.9041 0.0750 80 L 0.0272 0.8732 0.0997 81 T 0.0269 0.8487 0.1244 82 L 0.0429 0.7669 0.1902 83 A 0.0878 0.6524 0.2598 84 V 0.1288 0.5170 0.3542 85 A 0.1140 0.1531 0.7328 86 P 0.0542 0.2334 0.7124 87 V 0.0101 0.8723 0.1176 88 K 0.0095 0.9053 0.0853 89 A 0.0053 0.9447 0.0501 90 R 0.0048 0.9545 0.0407 91 E 0.0047 0.9571 0.0382 92 Q 0.0047 0.9562 0.0390 93 L 0.0047 0.9553 0.0400 94 E 0.0047 0.9565 0.0387 95 A 0.0049 0.9523 0.0428 96 I 0.0053 0.9366 0.0582 97 V 0.0083 0.8840 0.1077 98 S 0.0134 0.6571 0.3295 99 S 0.0331 0.4075 0.5594 100 K 0.0444 0.1959 0.7597 101 W 0.0733 0.1395 0.7872 102 F 0.1076 0.0488 0.8436 103 P 0.0857 0.0777 0.8366 104 Q 0.0683 0.1334 0.7983 105 A 0.0649 0.2026 0.7326 106 G 0.0562 0.1972 0.7466 107 D 0.0669 0.3010 0.6321 108 A 0.0233 0.7672 0.2095 109 G 0.0144 0.8227 0.1629 110 M 0.0227 0.8510 0.1263 111 C 0.0268 0.8731 0.1002 112 L 0.0176 0.8796 0.1028 113 D 0.0189 0.8285 0.1526 114 L 0.0214 0.7959 0.1827 115 L 0.0734 0.5611 0.3655 116 D 0.0801 0.3777 0.5422 117 D 0.0638 0.1764 0.7599 118 G 0.0858 0.0670 0.8472 119 T 0.2900 0.0427 0.6673 120 F 0.4765 0.0192 0.5043 121 K 0.3181 0.0153 0.6666 122 P 0.1340 0.0434 0.8226 123 K 0.0527 0.0445 0.9029