# This file is the result of combining several RDB files, specifically # T0459.t04.dssp-ebghstl.rdb (weight 1.53986) # T0459.t04.stride-ebghtl.rdb (weight 1.24869) # T0459.t04.str2.rdb (weight 1.54758) # T0459.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 T0459.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0459 # 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 T0459.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 212.154 # # ============================================ # Comments from T0459.t04.stride-ebghtl.rdb # ============================================ # TARGET T0459 # 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 T0459.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 212.154 # # ============================================ # Comments from T0459.t04.str2.rdb # ============================================ # TARGET T0459 # 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 T0459.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 212.154 # # ============================================ # Comments from T0459.t04.alpha.rdb # ============================================ # TARGET T0459 # 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 T0459.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 212.154 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0597 0.0753 0.8650 2 N 0.0703 0.2727 0.6570 3 A 0.0987 0.3671 0.5342 4 M 0.1422 0.4347 0.4230 5 L 0.1919 0.3258 0.4822 6 R 0.1989 0.2120 0.5891 7 Y 0.1262 0.1667 0.7071 8 G 0.0834 0.0952 0.8214 9 D 0.0719 0.1318 0.7963 10 T 0.0790 0.2277 0.6932 11 E 0.0793 0.2603 0.6604 12 I 0.0914 0.2174 0.6911 13 C 0.0880 0.0985 0.8135 14 I 0.0581 0.1813 0.7606 15 D 0.0613 0.2034 0.7354 16 P 0.0209 0.6279 0.3511 17 S 0.0062 0.9286 0.0653 18 E 0.0047 0.9567 0.0386 19 S 0.0047 0.9587 0.0365 20 V 0.0047 0.9586 0.0367 21 L 0.0047 0.9578 0.0375 22 H 0.0048 0.9536 0.0416 23 L 0.0057 0.9359 0.0584 24 L 0.0110 0.8612 0.1278 25 G 0.0283 0.5231 0.4487 26 K 0.0197 0.5130 0.4673 27 K 0.0415 0.6285 0.3300 28 Y 0.1044 0.5697 0.3258 29 T 0.1323 0.7179 0.1499 30 M 0.1724 0.7464 0.0812 31 L 0.1164 0.8105 0.0731 32 I 0.0993 0.8421 0.0585 33 I 0.0613 0.8803 0.0583 34 S 0.0483 0.8855 0.0662 35 V 0.0268 0.9024 0.0708 36 L 0.0262 0.8114 0.1624 37 G 0.0456 0.4985 0.4559 38 N 0.0562 0.1768 0.7670 39 G 0.0443 0.0527 0.9029 40 S 0.0565 0.0832 0.8603 41 T 0.0818 0.0956 0.8226 42 R 0.0727 0.1011 0.8262 43 Q 0.0677 0.1748 0.7574 44 N 0.0693 0.2370 0.6936 45 F 0.0155 0.7983 0.1862 46 N 0.0083 0.8973 0.0944 47 D 0.0069 0.9160 0.0771 48 I 0.0081 0.9102 0.0817 49 R 0.0085 0.8880 0.1035 50 S 0.0114 0.7724 0.2161 51 S 0.0173 0.5927 0.3901 52 I 0.0648 0.1330 0.8022 53 P 0.0189 0.1952 0.7860 54 G 0.0214 0.1716 0.8070 55 I 0.0618 0.3566 0.5816 56 S 0.0370 0.5711 0.3920 57 S 0.0047 0.9497 0.0456 58 T 0.0047 0.9589 0.0364 59 I 0.0047 0.9591 0.0362 60 L 0.0047 0.9568 0.0385 61 S 0.0047 0.9577 0.0376 62 R 0.0047 0.9543 0.0410 63 R 0.0047 0.9519 0.0434 64 I 0.0047 0.9567 0.0386 65 K 0.0047 0.9588 0.0366 66 D 0.0047 0.9581 0.0373 67 L 0.0047 0.9561 0.0392 68 I 0.0049 0.9370 0.0581 69 D 0.0059 0.8468 0.1473 70 S 0.0423 0.3458 0.6119 71 G 0.0363 0.0404 0.9233 72 L 0.2013 0.0407 0.7580 73 V 0.7124 0.0249 0.2627 74 E 0.7916 0.0188 0.1896 75 R 0.7682 0.0165 0.2152 76 R 0.6459 0.0166 0.3375 77 S 0.2973 0.0273 0.6754 78 G 0.1364 0.0164 0.8471 79 Q 0.2595 0.0154 0.7251 80 I 0.6514 0.0076 0.3411 81 T 0.8154 0.0053 0.1793 82 T 0.8932 0.0050 0.1019 83 Y 0.9107 0.0053 0.0839 84 A 0.9012 0.0069 0.0919 85 L 0.8001 0.0170 0.1829 86 T 0.3833 0.0325 0.5842 87 E 0.0572 0.3225 0.6203 88 K 0.0408 0.3119 0.6473 89 G 0.0388 0.4242 0.5370 90 M 0.0739 0.5359 0.3902 91 N 0.1014 0.5605 0.3381 92 V 0.0247 0.7741 0.2012 93 R 0.0167 0.8270 0.1563 94 N 0.0080 0.8788 0.1132 95 S 0.0061 0.8980 0.0958 96 L 0.0052 0.9376 0.0572 97 M 0.0047 0.9564 0.0389 98 P 0.0047 0.9566 0.0388 99 L 0.0048 0.9535 0.0418 100 L 0.0047 0.9518 0.0435 101 Q 0.0048 0.9311 0.0641 102 Y 0.0052 0.9033 0.0915 103 I 0.0077 0.8752 0.1171 104 S 0.0142 0.8171 0.1688 105 V 0.0213 0.7914 0.1873 106 L 0.0522 0.6998 0.2480 107 D 0.0410 0.6363 0.3227 108 R 0.0373 0.5452 0.4174 109 N 0.0530 0.2316 0.7154 110 G 0.0385 0.0452 0.9163 111 D 0.0535 0.0239 0.9226