# This file is the result of combining several RDB files, specifically # T0382.t06.dssp-ebghstl.rdb (weight 1.53986) # T0382.t06.stride-ebghtl.rdb (weight 1.24869) # T0382.t06.str2.rdb (weight 1.54758) # T0382.t06.alpha.rdb (weight 0.659012) # T0382.t04.dssp-ebghstl.rdb (weight 1.53986) # T0382.t04.stride-ebghtl.rdb (weight 1.24869) # T0382.t04.str2.rdb (weight 1.54758) # T0382.t04.alpha.rdb (weight 0.659012) # T0382.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0382.t2k.stride-ebghtl.rdb (weight 1.24869) # T0382.t2k.str2.rdb (weight 1.54758) # T0382.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 T0382.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.stride-ebghtl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.str2.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t06.alpha.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.stride-ebghtl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.str2.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.alpha.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 10 # # ============================================ # Comments from T0382.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 10 # # ============================================ # Comments from T0382.t2k.str2.rdb # ============================================ # TARGET T0382 # 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 T0382.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 10 # # ============================================ # Comments from T0382.t2k.alpha.rdb # ============================================ # TARGET T0382 # 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 T0382.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 10 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0673 0.0412 0.8915 2 S 0.1037 0.0645 0.8318 3 K 0.0818 0.2288 0.6894 4 L 0.0628 0.3106 0.6266 5 D 0.0796 0.3216 0.5988 6 L 0.0982 0.3888 0.5130 7 H 0.1305 0.3407 0.5288 8 Q 0.2563 0.2210 0.5227 9 M 0.2848 0.0794 0.6358 10 T 0.2258 0.0491 0.7251 11 T 0.0110 0.8838 0.1051 12 Q 0.0049 0.9471 0.0480 13 D 0.0048 0.9513 0.0438 14 L 0.0048 0.9553 0.0399 15 V 0.0047 0.9564 0.0389 16 A 0.0047 0.9576 0.0378 17 L 0.0047 0.9564 0.0389 18 F 0.0047 0.9555 0.0398 19 A 0.0047 0.9530 0.0422 20 K 0.0049 0.9480 0.0471 21 V 0.0060 0.9339 0.0601 22 T 0.0107 0.9005 0.0888 23 V 0.0100 0.8959 0.0941 24 E 0.0155 0.8692 0.1153 25 Q 0.0256 0.8471 0.1273 26 D 0.0274 0.8264 0.1463 27 D 0.0330 0.8304 0.1366 28 A 0.0460 0.8137 0.1403 29 L 0.0722 0.7393 0.1885 30 L 0.0679 0.6578 0.2744 31 G 0.0380 0.6824 0.2796 32 N 0.0319 0.6399 0.3282 33 Q 0.0285 0.6885 0.2830 34 I 0.0165 0.8525 0.1310 35 S 0.0139 0.8721 0.1140 36 R 0.0120 0.8910 0.0971 37 F 0.0112 0.8989 0.0899 38 N 0.0092 0.9069 0.0839 39 R 0.0060 0.9274 0.0666 40 L 0.0053 0.9359 0.0588 41 F 0.0049 0.9451 0.0499 42 G 0.0050 0.9426 0.0525 43 V 0.0051 0.9392 0.0557 44 M 0.0050 0.9488 0.0462 45 A 0.0049 0.9485 0.0466 46 E 0.0048 0.9517 0.0435 47 I 0.0048 0.9519 0.0433 48 A 0.0048 0.9533 0.0419 49 D 0.0048 0.9486 0.0466 50 E 0.0050 0.9393 0.0557 51 L 0.0058 0.9140 0.0801 52 K 0.0077 0.8044 0.1880 53 A 0.0140 0.5510 0.4350 54 R 0.0439 0.1617 0.7944 55 D 0.0323 0.1549 0.8128 56 G 0.0222 0.2744 0.7034 57 D 0.0428 0.4950 0.4622 58 Q 0.0185 0.8143 0.1672 59 R 0.0100 0.9103 0.0797 60 T 0.0097 0.9321 0.0582 61 A 0.0103 0.9307 0.0590 62 L 0.0085 0.9369 0.0546 63 L 0.0075 0.9335 0.0590 64 S 0.0065 0.9208 0.0728 65 L 0.0078 0.8768 0.1154 66 F 0.0193 0.6390 0.3418 67 E 0.0245 0.3512 0.6243 68 Y 0.0666 0.1554 0.7779 69 P 0.0195 0.2143 0.7661 70 N 0.0388 0.1866 0.7746 71 M 0.0532 0.6099 0.3369 72 Q 0.0750 0.7601 0.1648 73 V 0.0488 0.8577 0.0935 74 R 0.0285 0.9008 0.0707 75 L 0.0117 0.9371 0.0511 76 Q 0.0075 0.9453 0.0472 77 A 0.0081 0.9463 0.0456 78 A 0.0066 0.9481 0.0453 79 K 0.0073 0.9338 0.0588 80 L 0.0073 0.9264 0.0663 81 T 0.0153 0.8679 0.1168 82 L 0.0317 0.7028 0.2655 83 A 0.1041 0.4947 0.4012 84 V 0.1723 0.2636 0.5641 85 A 0.1078 0.0454 0.8468 86 P 0.0370 0.3717 0.5912 87 V 0.0055 0.9291 0.0654 88 K 0.0051 0.9335 0.0614 89 A 0.0048 0.9514 0.0437 90 R 0.0047 0.9574 0.0379 91 E 0.0048 0.9558 0.0394 92 Q 0.0048 0.9550 0.0402 93 L 0.0047 0.9557 0.0396 94 E 0.0048 0.9554 0.0398 95 A 0.0049 0.9503 0.0448 96 I 0.0057 0.9309 0.0634 97 V 0.0111 0.8695 0.1194 98 S 0.0148 0.6518 0.3335 99 S 0.0424 0.3939 0.5637 100 K 0.0481 0.1460 0.8059 101 W 0.0786 0.1067 0.8147 102 F 0.1123 0.0612 0.8265 103 P 0.0920 0.0623 0.8457 104 Q 0.0807 0.0908 0.8285 105 A 0.0496 0.2294 0.7210 106 G 0.0523 0.2391 0.7086 107 D 0.0597 0.3827 0.5576 108 A 0.0324 0.7054 0.2622 109 G 0.0350 0.7770 0.1880 110 M 0.0491 0.8239 0.1271 111 C 0.0482 0.8631 0.0887 112 L 0.0586 0.8495 0.0919 113 D 0.0754 0.8029 0.1217 114 L 0.0716 0.7455 0.1829 115 L 0.0804 0.6311 0.2884 116 D 0.0700 0.4581 0.4718 117 D 0.0811 0.2224 0.6966 118 G 0.1209 0.0869 0.7922 119 T 0.2502 0.0685 0.6814 120 F 0.4077 0.0425 0.5498 121 K 0.2721 0.0265 0.7014 122 P 0.1302 0.0208 0.8490 123 K 0.0415 0.0400 0.9184