# This file is the result of combining several RDB files, specifically # T0327.t06.dssp-ebghstl.rdb (weight 1.53986) # T0327.t06.stride-ebghtl.rdb (weight 1.24869) # T0327.t06.str2.rdb (weight 1.54758) # T0327.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 T0327.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.str2.rdb # ============================================ # TARGET T0327 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0725 0.2498 0.6778 2 N 0.0733 0.2412 0.6856 3 K 0.0314 0.4283 0.5402 4 D 0.0339 0.4165 0.5495 5 K 0.0418 0.6900 0.2682 6 L 0.0922 0.6921 0.2157 7 R 0.0694 0.8193 0.1113 8 Y 0.0641 0.8726 0.0633 9 A 0.0343 0.9186 0.0471 10 I 0.0344 0.9204 0.0452 11 L 0.0270 0.9181 0.0549 12 K 0.0118 0.9425 0.0457 13 E 0.0112 0.9395 0.0493 14 I 0.0145 0.8993 0.0863 15 F 0.0332 0.7742 0.1926 16 E 0.0660 0.3977 0.5363 17 G 0.0455 0.1310 0.8235 18 N 0.0508 0.0537 0.8955 19 T 0.0717 0.0227 0.9057 20 P 0.0895 0.0456 0.8648 21 L 0.0956 0.0769 0.8276 22 S 0.0848 0.0878 0.8274 23 E 0.0347 0.4847 0.4807 24 N 0.0410 0.3716 0.5873 25 D 0.0518 0.3455 0.6027 26 I 0.1058 0.1804 0.7138 27 G 0.0976 0.0734 0.8290 28 V 0.1711 0.0303 0.7986 29 T 0.0888 0.0305 0.8806 30 E 0.0078 0.8534 0.1389 31 D 0.0060 0.8677 0.1263 32 Q 0.0069 0.9056 0.0875 33 F 0.0060 0.9399 0.0541 34 D 0.0047 0.9511 0.0442 35 D 0.0047 0.9520 0.0432 36 A 0.0047 0.9566 0.0387 37 V 0.0047 0.9590 0.0364 38 N 0.0047 0.9566 0.0388 39 F 0.0047 0.9470 0.0483 40 L 0.0073 0.9343 0.0584 41 K 0.0083 0.8654 0.1263 42 R 0.0108 0.6556 0.3336 43 E 0.0446 0.2019 0.7535 44 G 0.0351 0.0275 0.9374 45 Y 0.2505 0.0145 0.7350 46 I 0.7966 0.0061 0.1973 47 I 0.7814 0.0286 0.1900 48 G 0.8207 0.0109 0.1684 49 V 0.8437 0.0055 0.1508 50 H 0.8713 0.0040 0.1247 51 Y 0.7389 0.0094 0.2517 52 S 0.2496 0.0220 0.7285 53 D 0.0314 0.1040 0.8647 54 D 0.0326 0.0577 0.9097 55 R 0.0905 0.0384 0.8711 56 P 0.1593 0.0927 0.7480 57 H 0.4548 0.1577 0.3875 58 L 0.5726 0.1839 0.2434 59 Y 0.5193 0.2000 0.2807 60 K 0.4701 0.1331 0.3968 61 L 0.2912 0.0965 0.6124 62 G 0.1224 0.0498 0.8278 63 P 0.0499 0.2748 0.6754 64 E 0.0787 0.3020 0.6193 65 L 0.1818 0.2324 0.5858 66 T 0.1321 0.1534 0.7145 67 E 0.0605 0.5268 0.4127 68 K 0.0432 0.4778 0.4790 69 G 0.0265 0.6049 0.3686 70 E 0.0229 0.8285 0.1486 71 N 0.0150 0.8636 0.1214 72 Y 0.0093 0.8728 0.1179 73 L 0.0259 0.7950 0.1791 74 K 0.0159 0.7240 0.2601 75 E 0.0165 0.5230 0.4605 76 N 0.0536 0.2952 0.6512 77 G 0.0302 0.4665 0.5033 78 T 0.0339 0.5557 0.4105 79 W 0.0186 0.8194 0.1620 80 S 0.0115 0.8806 0.1079 81 K 0.0058 0.9434 0.0508 82 A 0.0052 0.9533 0.0415 83 Y 0.0058 0.9498 0.0444 84 K 0.0057 0.9471 0.0472 85 T 0.0062 0.9439 0.0499 86 I 0.0066 0.9411 0.0524 87 K 0.0070 0.9456 0.0474 88 E 0.0062 0.9429 0.0509 89 I 0.0082 0.9189 0.0729 90 K 0.0077 0.9073 0.0850 91 D 0.0144 0.8334 0.1522 92 W 0.0310 0.7486 0.2205 93 I 0.1155 0.4058 0.4787 94 K 0.1342 0.3094 0.5564 95 L 0.0712 0.5035 0.4253 96 E 0.1039 0.4718 0.4242 97 H 0.1136 0.4317 0.4546 98 H 0.1041 0.3184 0.5774 99 H 0.1056 0.2197 0.6746 100 H 0.1140 0.1725 0.7135 101 H 0.1099 0.1144 0.7757 102 H 0.0623 0.0568 0.8809