# This file is the result of combining several RDB files, specifically # T0354.t04.dssp-ebghstl.rdb (weight 1.53986) # T0354.t04.stride-ebghtl.rdb (weight 1.24869) # T0354.t04.str2.rdb (weight 1.54758) # T0354.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 T0354.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.stride-ebghtl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.str2.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.alpha.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0806 0.0152 0.9042 2 E 0.0818 0.0651 0.8531 3 I 0.0089 0.8794 0.1116 4 Q 0.0053 0.9467 0.0480 5 E 0.0048 0.9544 0.0408 6 I 0.0047 0.9585 0.0368 7 S 0.0047 0.9608 0.0345 8 K 0.0046 0.9614 0.0340 9 L 0.0046 0.9606 0.0348 10 A 0.0047 0.9590 0.0363 11 I 0.0047 0.9594 0.0359 12 E 0.0048 0.9561 0.0391 13 A 0.0051 0.9459 0.0490 14 L 0.0055 0.9262 0.0683 15 E 0.0078 0.8568 0.1353 16 D 0.0131 0.7162 0.2707 17 I 0.0689 0.4577 0.4733 18 K 0.0647 0.1249 0.8104 19 G 0.1015 0.1607 0.7379 20 K 0.1093 0.2010 0.6897 21 D 0.3235 0.0852 0.5913 22 I 0.6638 0.0298 0.3064 23 I 0.8555 0.0170 0.1275 24 E 0.9030 0.0092 0.0878 25 L 0.8250 0.0094 0.1655 26 D 0.6432 0.0087 0.3482 27 T 0.2137 0.1574 0.6289 28 S 0.0561 0.2371 0.7068 29 K 0.0546 0.2891 0.6563 30 L 0.1288 0.2834 0.5878 31 T 0.1614 0.2955 0.5431 32 S 0.1871 0.3342 0.4787 33 L 0.3015 0.2932 0.4053 34 F 0.4494 0.1205 0.4301 35 Q 0.4187 0.1168 0.4645 36 R 0.8180 0.0355 0.1465 37 M 0.9127 0.0123 0.0750 38 I 0.9230 0.0089 0.0681 39 V 0.9020 0.0108 0.0872 40 A 0.7524 0.0218 0.2258 41 T 0.3963 0.0292 0.5745 42 G 0.1246 0.0613 0.8141 43 D 0.1029 0.0657 0.8314 44 S 0.0465 0.4542 0.4992 45 N 0.0053 0.9082 0.0865 46 R 0.0051 0.9486 0.0463 47 Q 0.0047 0.9572 0.0381 48 V 0.0047 0.9598 0.0355 49 K 0.0047 0.9607 0.0346 50 A 0.0047 0.9597 0.0355 51 L 0.0048 0.9563 0.0389 52 A 0.0047 0.9589 0.0364 53 N 0.0048 0.9579 0.0374 54 S 0.0047 0.9575 0.0378 55 V 0.0047 0.9580 0.0373 56 Q 0.0047 0.9603 0.0350 57 V 0.0047 0.9607 0.0347 58 K 0.0047 0.9609 0.0344 59 L 0.0047 0.9583 0.0370 60 K 0.0049 0.9499 0.0452 61 E 0.0057 0.9237 0.0706 62 A 0.0408 0.4685 0.4907 63 G 0.0341 0.0278 0.9382 64 V 0.1104 0.0145 0.8751 65 D 0.3563 0.0201 0.6236 66 I 0.5097 0.0505 0.4399 67 V 0.4954 0.0818 0.4228 68 G 0.4748 0.0795 0.4457 69 S 0.5448 0.0757 0.3794 70 E 0.5824 0.0511 0.3665 71 G 0.4832 0.0345 0.4824 72 H 0.3410 0.0532 0.6058 73 E 0.2631 0.0849 0.6521 74 S 0.1032 0.0565 0.8403 75 G 0.1305 0.0362 0.8334 76 E 0.4962 0.0110 0.4928 77 W 0.9033 0.0033 0.0935 78 V 0.9283 0.0035 0.0683 79 L 0.9320 0.0031 0.0649 80 V 0.9037 0.0050 0.0912 81 D 0.7176 0.0087 0.2737 82 A 0.1811 0.0670 0.7519 83 G 0.0697 0.0459 0.8844 84 D 0.2133 0.0428 0.7440 85 V 0.8082 0.0076 0.1842 86 V 0.9217 0.0048 0.0735 87 V 0.9213 0.0080 0.0707 88 H 0.8560 0.0324 0.1116 89 V 0.6368 0.0329 0.3303 90 M 0.4645 0.0420 0.4935 91 L 0.2299 0.0416 0.7285 92 P 0.0280 0.6686 0.3035 93 A 0.0278 0.6770 0.2952 94 V 0.0333 0.7282 0.2385 95 R 0.0622 0.6631 0.2746 96 D 0.0543 0.6039 0.3418 97 Y 0.0953 0.6046 0.3001 98 Y 0.1566 0.4769 0.3665 99 D 0.1221 0.3986 0.4793 100 I 0.0058 0.9242 0.0699 101 E 0.0061 0.9281 0.0658 102 A 0.0066 0.9137 0.0798 103 L 0.0109 0.8482 0.1409 104 W 0.0214 0.6573 0.3213 105 G 0.0406 0.3286 0.6308 106 G 0.0327 0.1182 0.8491 107 Q 0.0588 0.0459 0.8953 108 K 0.0704 0.0326 0.8970 109 P 0.0786 0.2018 0.7196 110 S 0.1102 0.3737 0.5161 111 F 0.1353 0.4215 0.4431 112 A 0.1632 0.4101 0.4266 113 V 0.1422 0.3555 0.5023 114 G 0.0949 0.2339 0.6712 115 A 0.1026 0.1634 0.7340 116 A 0.1057 0.1186 0.7757 117 K 0.0837 0.0524 0.8639 118 P 0.0701 0.1426 0.7873 119 W 0.0619 0.3062 0.6319 120 S 0.0827 0.3980 0.5193 121 A 0.0974 0.4633 0.4393 122 V 0.1481 0.4485 0.4034 123 L 0.1757 0.3673 0.4570 124 E 0.1431 0.3193 0.5376 125 H 0.1137 0.2818 0.6045 126 H 0.0846 0.2124 0.7030 127 H 0.0672 0.1974 0.7354 128 H 0.0654 0.1575 0.7771 129 H 0.0685 0.0936 0.8378 130 H 0.0534 0.0484 0.8982