# This file is the result of combining several RDB files, specifically # T0352.t04.dssp-ebghstl.rdb (weight 1.53986) # T0352.t04.stride-ebghtl.rdb (weight 1.24869) # T0352.t04.str2.rdb (weight 1.54758) # T0352.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 T0352.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4528 # # ============================================ # Comments from T0352.t04.stride-ebghtl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4528 # # ============================================ # Comments from T0352.t04.str2.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4528 # # ============================================ # Comments from T0352.t04.alpha.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4528 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0661 0.0230 0.9110 2 T 0.0651 0.0700 0.8649 3 T 0.0303 0.4974 0.4723 4 H 0.0150 0.8116 0.1733 5 D 0.0063 0.9280 0.0657 6 R 0.0055 0.9470 0.0475 7 V 0.0047 0.9568 0.0385 8 R 0.0047 0.9603 0.0351 9 L 0.0047 0.9563 0.0390 10 Q 0.0047 0.9540 0.0413 11 L 0.0047 0.9600 0.0353 12 Q 0.0046 0.9614 0.0339 13 A 0.0046 0.9611 0.0343 14 L 0.0047 0.9597 0.0356 15 E 0.0047 0.9606 0.0347 16 A 0.0046 0.9597 0.0356 17 L 0.0047 0.9561 0.0392 18 L 0.0047 0.9481 0.0472 19 R 0.0049 0.9129 0.0823 20 E 0.0061 0.8486 0.1453 21 H 0.0380 0.6116 0.3503 22 Q 0.0236 0.3398 0.6366 23 H 0.0554 0.3121 0.6326 24 W 0.1254 0.2990 0.5756 25 R 0.1226 0.2356 0.6419 26 N 0.0974 0.1349 0.7678 27 D 0.0743 0.0458 0.8799 28 E 0.0734 0.0196 0.9070 29 P 0.0801 0.0168 0.9031 30 Q 0.0732 0.0277 0.8991 31 P 0.0097 0.7715 0.2188 32 H 0.0112 0.7967 0.1921 33 Q 0.0154 0.8117 0.1728 34 F 0.0748 0.5455 0.3798 35 N 0.0556 0.2888 0.6555 36 S 0.0765 0.1156 0.8080 37 T 0.0661 0.1050 0.8289 38 Q 0.0929 0.0390 0.8681 39 P 0.1595 0.0714 0.7691 40 F 0.4529 0.0965 0.4506 41 F 0.5394 0.1106 0.3500 42 M 0.4872 0.1284 0.3844 43 D 0.3834 0.1106 0.5060 44 T 0.1920 0.1202 0.6877 45 M 0.1127 0.0898 0.7975 46 E 0.0805 0.1517 0.7678 47 P 0.0135 0.8091 0.1774 48 L 0.0173 0.8375 0.1452 49 E 0.0145 0.8908 0.0947 50 W 0.0222 0.8990 0.0788 51 L 0.0249 0.8922 0.0829 52 Q 0.0126 0.9323 0.0550 53 W 0.0126 0.9379 0.0495 54 V 0.0211 0.9054 0.0735 55 L 0.0213 0.8917 0.0870 56 I 0.0271 0.8527 0.1202 57 P 0.0144 0.8464 0.1392 58 R 0.0158 0.8233 0.1609 59 M 0.0049 0.9440 0.0511 60 H 0.0048 0.9526 0.0426 61 D 0.0047 0.9573 0.0380 62 L 0.0050 0.9529 0.0421 63 L 0.0052 0.9378 0.0570 64 D 0.0063 0.8556 0.1381 65 N 0.0427 0.5119 0.4454 66 K 0.0309 0.1785 0.7906 67 Q 0.0589 0.0216 0.9195 68 P 0.1016 0.0295 0.8689 69 L 0.0880 0.0235 0.8885 70 P 0.0578 0.0925 0.8497 71 G 0.0277 0.1915 0.7808 72 A 0.0813 0.3117 0.6070 73 F 0.1784 0.2765 0.5451 74 A 0.2894 0.2487 0.4620 75 V 0.2085 0.3622 0.4293 76 A 0.0718 0.6485 0.2797 77 P 0.0232 0.8777 0.0991 78 Y 0.0192 0.9115 0.0693 79 Y 0.0112 0.9423 0.0464 80 E 0.0103 0.9445 0.0451 81 M 0.0066 0.9473 0.0460 82 A 0.0071 0.9294 0.0634 83 L 0.0115 0.8709 0.1176 84 A 0.0149 0.7351 0.2500 85 T 0.0303 0.4881 0.4816 86 D 0.0398 0.2712 0.6890 87 H 0.0452 0.2313 0.7236 88 P 0.0185 0.5470 0.4345 89 Q 0.0151 0.7588 0.2261 90 R 0.0097 0.8923 0.0980 91 A 0.0072 0.9379 0.0549 92 L 0.0067 0.9445 0.0488 93 I 0.0054 0.9506 0.0440 94 L 0.0047 0.9589 0.0364 95 A 0.0047 0.9589 0.0364 96 E 0.0047 0.9560 0.0393 97 L 0.0047 0.9568 0.0385 98 E 0.0049 0.9554 0.0397 99 K 0.0049 0.9509 0.0442 100 L 0.0048 0.9519 0.0433 101 D 0.0050 0.9509 0.0441 102 A 0.0049 0.9443 0.0508 103 L 0.0059 0.9120 0.0821 104 F 0.0116 0.7598 0.2285 105 A 0.0213 0.5230 0.4557 106 D 0.0374 0.3280 0.6347 107 D 0.0363 0.3864 0.5773 108 A 0.0247 0.5527 0.4227 109 S 0.0431 0.6066 0.3503 110 L 0.0528 0.6512 0.2960 111 E 0.0589 0.6055 0.3356 112 H 0.0711 0.5201 0.4088 113 H 0.0734 0.3892 0.5374 114 H 0.0804 0.2759 0.6437 115 H 0.0794 0.2039 0.7167 116 H 0.0735 0.1200 0.8065 117 H 0.0551 0.0475 0.8974