# This file is the result of combining several RDB files, specifically # T0254.t04.dssp-ebghstl.rdb (weight 1.53986) # T0254.t04.stride-ebghtl.rdb (weight 1.24869) # T0254.t04.str2.rdb (weight 1.54758) # T0254.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 T0254.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0254 # 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 T0254.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 10.1529 # # ============================================ # Comments from T0254.t04.stride-ebghtl.rdb # ============================================ # TARGET T0254 # 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 T0254.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 10.1529 # # ============================================ # Comments from T0254.t04.str2.rdb # ============================================ # TARGET T0254 # 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 T0254.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 10.1529 # # ============================================ # Comments from T0254.t04.alpha.rdb # ============================================ # TARGET T0254 # 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 T0254.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 10.1529 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0770 0.0165 0.9066 2 P 0.1766 0.0222 0.8012 3 H 0.6332 0.0415 0.3252 4 L 0.8214 0.0258 0.1527 5 R 0.8342 0.0301 0.1358 6 F 0.7682 0.0527 0.1791 7 R 0.5976 0.1062 0.2962 8 A 0.4083 0.2170 0.3748 9 V 0.2944 0.3135 0.3921 10 E 0.1587 0.5325 0.3088 11 A 0.0193 0.8737 0.1071 12 H 0.0131 0.8914 0.0955 13 I 0.0115 0.9173 0.0712 14 V 0.0097 0.9310 0.0593 15 E 0.0093 0.9194 0.0713 16 S 0.0101 0.8689 0.1210 17 L 0.0126 0.7731 0.2143 18 V 0.0125 0.7542 0.2333 19 P 0.0048 0.9513 0.0439 20 T 0.0048 0.9502 0.0450 21 L 0.0048 0.9541 0.0411 22 L 0.0047 0.9554 0.0399 23 N 0.0048 0.9500 0.0452 24 E 0.0053 0.9283 0.0663 25 L 0.0052 0.9340 0.0608 26 S 0.0052 0.9381 0.0567 27 S 0.0051 0.9262 0.0687 28 L 0.0077 0.8766 0.1156 29 L 0.0268 0.7508 0.2224 30 S 0.0465 0.3667 0.5868 31 T 0.0968 0.0971 0.8061 32 A 0.0842 0.0543 0.8615 33 R 0.0462 0.4222 0.5316 34 N 0.0569 0.3420 0.6011 35 A 0.3769 0.1729 0.4502 36 F 0.7867 0.0093 0.2039 37 T 0.9066 0.0058 0.0876 38 F 0.9134 0.0053 0.0814 39 E 0.8909 0.0070 0.1021 40 L 0.8323 0.0078 0.1599 41 I 0.6262 0.0269 0.3469 42 N 0.3461 0.0322 0.6217 43 T 0.3058 0.0529 0.6413 44 Q 0.5468 0.0682 0.3850 45 Y 0.7629 0.0502 0.1868 46 F 0.7415 0.0568 0.2018 47 A 0.6049 0.0762 0.3189 48 E 0.3128 0.0820 0.6051 49 G 0.1153 0.0676 0.8172 50 G 0.1519 0.0568 0.7913 51 V 0.3950 0.0271 0.5779 52 Y 0.4309 0.0094 0.5597 53 P 0.5135 0.0060 0.4806 54 M 0.8587 0.0064 0.1349 55 V 0.9162 0.0038 0.0800 56 E 0.9237 0.0036 0.0727 57 V 0.9148 0.0036 0.0816 58 L 0.8388 0.0128 0.1484 59 W 0.7082 0.0157 0.2760 60 F 0.3483 0.0399 0.6118 61 G 0.1389 0.0545 0.8066 62 R 0.0687 0.1560 0.7753 63 E 0.0598 0.2846 0.6556 64 Q 0.0110 0.8217 0.1673 65 Q 0.0119 0.8899 0.0982 66 T 0.0076 0.9256 0.0668 67 Q 0.0047 0.9572 0.0381 68 D 0.0048 0.9605 0.0347 69 Q 0.0047 0.9613 0.0341 70 I 0.0047 0.9610 0.0343 71 A 0.0046 0.9613 0.0340 72 Q 0.0046 0.9617 0.0336 73 V 0.0047 0.9603 0.0350 74 I 0.0047 0.9569 0.0383 75 T 0.0048 0.9589 0.0363 76 D 0.0047 0.9602 0.0351 77 Q 0.0047 0.9599 0.0354 78 I 0.0047 0.9566 0.0386 79 R 0.0048 0.9537 0.0415 80 Q 0.0056 0.9296 0.0648 81 L 0.0099 0.8738 0.1164 82 L 0.0539 0.5764 0.3698 83 G 0.0388 0.1203 0.8409 84 A 0.0370 0.1153 0.8477 85 D 0.0629 0.1112 0.8260 86 S 0.1011 0.0826 0.8163 87 H 0.3310 0.0248 0.6442 88 L 0.8293 0.0043 0.1664 89 A 0.9202 0.0035 0.0762 90 V 0.9324 0.0031 0.0645 91 V 0.9269 0.0037 0.0695 92 F 0.9144 0.0036 0.0820 93 I 0.8476 0.0091 0.1433 94 P 0.7438 0.0066 0.2496 95 L 0.4681 0.0350 0.4969 96 Q 0.2364 0.0334 0.7301 97 R 0.0599 0.2485 0.6916 98 T 0.1116 0.2599 0.6285 99 A 0.3698 0.2060 0.4242 100 Y 0.6280 0.0898 0.2822 101 Y 0.5761 0.0965 0.3274 102 L 0.4214 0.1025 0.4761 103 D 0.0718 0.0391 0.8891 104 G 0.0868 0.0361 0.8771 105 Q 0.3170 0.0280 0.6549 106 H 0.4621 0.0192 0.5187 107 F 0.1525 0.0228 0.8246