# This file is the result of combining several RDB files, specifically # T0343.t04.dssp-ebghstl.rdb (weight 1.53986) # T0343.t04.stride-ebghtl.rdb (weight 1.24869) # T0343.t04.str2.rdb (weight 1.54758) # T0343.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 T0343.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.stride-ebghtl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.str2.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t04.alpha.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1015 0.0351 0.8634 2 T 0.1328 0.1709 0.6963 3 W 0.0134 0.8998 0.0868 4 R 0.0100 0.9286 0.0614 5 E 0.0077 0.9488 0.0436 6 I 0.0078 0.9468 0.0454 7 L 0.0100 0.9321 0.0579 8 R 0.0163 0.8735 0.1102 9 K 0.0214 0.7840 0.1945 10 E 0.0484 0.3981 0.5535 11 G 0.0504 0.0974 0.8521 12 F 0.2847 0.0517 0.6636 13 L 0.6184 0.0304 0.3512 14 D 0.5626 0.0310 0.4064 15 L 0.2574 0.2631 0.4794 16 G 0.1357 0.1985 0.6658 17 E 0.2841 0.1409 0.5750 18 F 0.7810 0.0153 0.2038 19 I 0.9094 0.0050 0.0856 20 V 0.9249 0.0035 0.0716 21 E 0.9168 0.0069 0.0762 22 L 0.9258 0.0036 0.0706 23 V 0.9151 0.0057 0.0792 24 Y 0.9043 0.0048 0.0909 25 I 0.7530 0.0185 0.2285 26 D 0.3823 0.0275 0.5902 27 C 0.1593 0.0309 0.8099 28 P 0.0801 0.0920 0.8279 29 C 0.1141 0.0831 0.8028 30 E 0.1342 0.0477 0.8181 31 P 0.1700 0.0406 0.7895 32 I 0.1477 0.0165 0.8358 33 P 0.1135 0.0126 0.8739 34 P 0.1612 0.0234 0.8155 35 T 0.5370 0.0170 0.4461 36 L 0.9018 0.0041 0.0941 37 A 0.9267 0.0035 0.0698 38 I 0.9271 0.0036 0.0693 39 Y 0.8960 0.0056 0.0983 40 D 0.6098 0.0095 0.3807 41 K 0.1761 0.0729 0.7510 42 K 0.1304 0.0619 0.8077 43 G 0.0842 0.0554 0.8605 44 D 0.1460 0.0459 0.8081 45 E 0.6113 0.0353 0.3534 46 W 0.8423 0.0154 0.1423 47 Y 0.8693 0.0094 0.1213 48 K 0.8982 0.0081 0.0937 49 V 0.8058 0.0207 0.1736 50 E 0.6021 0.0526 0.3453 51 E 0.2965 0.0444 0.6592 52 A 0.1191 0.0313 0.8496 53 P 0.0747 0.0876 0.8377 54 N 0.0939 0.0931 0.8130 55 V 0.0921 0.2538 0.6541 56 Q 0.0774 0.3168 0.6058 57 N 0.1173 0.3691 0.5135 58 Y 0.0506 0.6944 0.2549 59 R 0.0215 0.8717 0.1068 60 E 0.0157 0.9071 0.0772 61 A 0.0123 0.9145 0.0732 62 V 0.0058 0.9458 0.0484 63 E 0.0047 0.9589 0.0364 64 W 0.0047 0.9571 0.0382 65 A 0.0047 0.9581 0.0372 66 I 0.0047 0.9604 0.0349 67 E 0.0046 0.9607 0.0347 68 V 0.0047 0.9580 0.0373 69 L 0.0047 0.9574 0.0379 70 E 0.0056 0.9530 0.0413 71 R 0.0070 0.9417 0.0513 72 I 0.0136 0.9052 0.0812 73 R 0.0333 0.7587 0.2080 74 D 0.0423 0.3188 0.6389 75 G 0.0317 0.0691 0.8992 76 E 0.0789 0.1024 0.8187 77 N 0.2250 0.0672 0.7078 78 V 0.3972 0.0542 0.5487 79 K 0.4934 0.0483 0.4583 80 L 0.7096 0.0475 0.2429 81 V 0.6811 0.0515 0.2675 82 S 0.6024 0.0426 0.3551 83 L 0.3981 0.0533 0.5486 84 D 0.1505 0.0558 0.7937 85 G 0.0610 0.0336 0.9055 86 P 0.0581 0.0431 0.8988 87 A 0.0778 0.0240 0.8983 88 P 0.0543 0.0349 0.9108 89 P 0.0066 0.8972 0.0962 90 K 0.0050 0.9444 0.0506 91 V 0.0048 0.9539 0.0413 92 M 0.0047 0.9579 0.0374 93 K 0.0047 0.9588 0.0365 94 R 0.0047 0.9562 0.0391 95 L 0.0048 0.9510 0.0442 96 S 0.0047 0.9526 0.0426 97 L 0.0048 0.9471 0.0481 98 A 0.0052 0.9319 0.0629 99 L 0.0053 0.9284 0.0662 100 Q 0.0064 0.8875 0.1060 101 K 0.0084 0.8226 0.1690 102 L 0.0245 0.6586 0.3169 103 T 0.0404 0.3144 0.6451 104 E 0.0265 0.1155 0.8580