# This file is the result of combining several RDB files, specifically # T0351.t06.dssp-ebghstl.rdb (weight 1.53986) # T0351.t06.stride-ebghtl.rdb (weight 1.24869) # T0351.t06.str2.rdb (weight 1.54758) # T0351.t06.alpha.rdb (weight 0.659012) # T0351.t04.dssp-ebghstl.rdb (weight 1.53986) # T0351.t04.stride-ebghtl.rdb (weight 1.24869) # T0351.t04.str2.rdb (weight 1.54758) # T0351.t04.alpha.rdb (weight 0.659012) # T0351.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0351.t2k.stride-ebghtl.rdb (weight 1.24869) # T0351.t2k.str2.rdb (weight 1.54758) # T0351.t2k.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 T0351.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0351 # 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 T0351.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 6 # # ============================================ # Comments from T0351.t06.stride-ebghtl.rdb # ============================================ # TARGET T0351 # Using neural net t06-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 T0351.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 6 # # ============================================ # Comments from T0351.t06.str2.rdb # ============================================ # TARGET T0351 # Using neural net t06-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 T0351.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 6 # # ============================================ # Comments from T0351.t06.alpha.rdb # ============================================ # TARGET T0351 # Using neural net t06-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 T0351.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 6 # # ============================================ # Comments from T0351.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t04.stride-ebghtl.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t04.str2.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t04.alpha.rdb # ============================================ # TARGET T0351 # 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 T0351.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 5 # # ============================================ # Comments from T0351.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0351 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0351.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0351.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0351 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0351.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0351.t2k.str2.rdb # ============================================ # TARGET T0351 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0351.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0351.t2k.alpha.rdb # ============================================ # TARGET T0351 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0351.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # 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 0.0658 0.0524 0.8819 2 I 0.1456 0.1450 0.7094 3 L 0.0586 0.6691 0.2723 4 Y 0.0573 0.7388 0.2040 5 D 0.0830 0.7421 0.1748 6 A 0.1300 0.7114 0.1586 7 I 0.1555 0.6516 0.1929 8 M 0.1955 0.5390 0.2655 9 Y 0.2263 0.4038 0.3698 10 K 0.2635 0.2744 0.4621 11 Y 0.1682 0.0722 0.7596 12 P 0.0530 0.1335 0.8135 13 N 0.0603 0.0971 0.8426 14 A 0.1610 0.0692 0.7699 15 V 0.2141 0.0464 0.7395 16 S 0.2255 0.0844 0.6900 17 R 0.1740 0.1555 0.6705 18 K 0.1930 0.1441 0.6630 19 D 0.3650 0.0668 0.5682 20 F 0.7073 0.0185 0.2742 21 E 0.8380 0.0102 0.1517 22 L 0.8480 0.0119 0.1401 23 R 0.7330 0.0193 0.2477 24 N 0.4397 0.0290 0.5314 25 D 0.1307 0.0470 0.8224 26 G 0.0709 0.0582 0.8709 27 N 0.0921 0.0381 0.8698 28 G 0.1553 0.0425 0.8022 29 S 0.3598 0.0587 0.5815 30 Y 0.6857 0.0560 0.2583 31 I 0.7297 0.0594 0.2108 32 E 0.6854 0.0928 0.2218 33 K 0.6990 0.0772 0.2238 34 W 0.6796 0.0581 0.2623 35 N 0.7176 0.0271 0.2553 36 L 0.6483 0.0439 0.3078 37 R 0.3977 0.0419 0.5604 38 A 0.1679 0.0216 0.8104 39 P 0.1069 0.0224 0.8708 40 L 0.1150 0.0223 0.8627 41 P 0.0963 0.0528 0.8509 42 T 0.0601 0.0769 0.8629 43 Q 0.0067 0.8815 0.1118 44 A 0.0056 0.9126 0.0818 45 E 0.0052 0.9271 0.0677 46 L 0.0051 0.9414 0.0536 47 E 0.0048 0.9465 0.0487 48 T 0.0048 0.9499 0.0452 49 W 0.0048 0.9484 0.0468 50 W 0.0048 0.9447 0.0505 51 E 0.0050 0.9367 0.0583 52 E 0.0056 0.9077 0.0867 53 L 0.0080 0.8532 0.1388 54 Q 0.0158 0.6692 0.3150 55 K 0.0233 0.4393 0.5375 56 N 0.0563 0.1049 0.8389 57 P 0.0564 0.1128 0.8308 58 P 0.0386 0.2023 0.7590 59 Y 0.0496 0.1981 0.7523 60 E 0.0525 0.1034 0.8440 61 P 0.0580 0.0809 0.8611 62 P 0.0311 0.6364 0.3325 63 D 0.0213 0.7293 0.2494 64 Q 0.0295 0.7915 0.1790 65 V 0.0231 0.8322 0.1447 66 E 0.0190 0.8512 0.1298 67 L 0.0169 0.8651 0.1180 68 L 0.0149 0.8699 0.1152 69 A 0.0142 0.8507 0.1351 70 Q 0.0185 0.8027 0.1788 71 E 0.0211 0.7492 0.2297 72 L 0.0287 0.6338 0.3375 73 S 0.0425 0.5660 0.3915 74 Q 0.0084 0.7706 0.2210 75 E 0.0108 0.8256 0.1637 76 K 0.0071 0.8686 0.1243 77 L 0.0078 0.8728 0.1194 78 A 0.0071 0.8866 0.1063 79 R 0.0058 0.8933 0.1008 80 K 0.0091 0.8690 0.1219 81 Q 0.0063 0.8887 0.1050 82 L 0.0057 0.9153 0.0789 83 E 0.0053 0.9264 0.0683 84 E 0.0052 0.9295 0.0653 85 L 0.0060 0.8934 0.1006 86 N 0.0072 0.8477 0.1451 87 K 0.0080 0.8327 0.1593 88 T 0.0104 0.8103 0.1794 89 L 0.0263 0.7768 0.1969 90 G 0.0195 0.6893 0.2912 91 N 0.0217 0.7550 0.2233 92 E 0.0171 0.7941 0.1888 93 L 0.0201 0.8025 0.1774 94 S 0.0216 0.7451 0.2334 95 D 0.0404 0.6311 0.3285 96 I 0.1427 0.4987 0.3587 97 K 0.3758 0.3222 0.3020 98 L 0.5076 0.2847 0.2078 99 S 0.5235 0.3004 0.1760 100 L 0.5852 0.2882 0.1266 101 L 0.5632 0.2835 0.1533 102 S 0.5708 0.2379 0.1913 103 L 0.4432 0.2573 0.2995 104 K 0.2601 0.1884 0.5515 105 G 0.1506 0.1569 0.6925 106 D 0.1762 0.2175 0.6063 107 Y 0.2404 0.3653 0.3943 108 A 0.2038 0.4499 0.3463 109 E 0.2076 0.4662 0.3262 110 L 0.1598 0.5125 0.3277 111 E 0.1456 0.4716 0.3828 112 H 0.1475 0.4267 0.4258 113 H 0.1415 0.3482 0.5103 114 H 0.1364 0.2674 0.5961 115 H 0.1187 0.1887 0.6926 116 H 0.0806 0.1066 0.8127 117 H 0.0438 0.0361 0.9201