# This file is the result of combining several RDB files, specifically # T0467.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0467.t2k.stride-ebghtl.rdb (weight 1.24869) # T0467.t2k.str.rdb (weight 1.53983) # 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 T0467.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ # Comments from T0467.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 86 # # ============================================ # Comments from T0467.t2k.str.rdb # ============================================ # TARGET T0467 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0467.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 86 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0406 0.0268 0.9326 2 D 0.1623 0.0508 0.7869 3 L 0.2467 0.1158 0.6374 4 N 0.3160 0.1282 0.5558 5 R 0.3762 0.0966 0.5271 6 M 0.3223 0.0801 0.5976 7 G 0.1978 0.0536 0.7487 8 K 0.1678 0.0376 0.7946 9 D 0.3392 0.0255 0.6353 10 E 0.5482 0.0192 0.4326 11 Y 0.6419 0.0125 0.3456 12 Y 0.7678 0.0095 0.2228 13 V 0.9014 0.0055 0.0930 14 Q 0.9422 0.0037 0.0542 15 I 0.9205 0.0035 0.0760 16 T 0.7854 0.0058 0.2088 17 V 0.4772 0.0174 0.5053 18 D 0.3921 0.0182 0.5896 19 G 0.6986 0.0074 0.2940 20 K 0.8812 0.0039 0.1150 21 E 0.9439 0.0031 0.0530 22 V 0.9380 0.0032 0.0588 23 H 0.9018 0.0037 0.0945 24 S 0.6856 0.0065 0.3079 25 K 0.4301 0.0189 0.5510 26 A 0.1678 0.0429 0.7893 27 D 0.1073 0.0560 0.8367 28 N 0.0869 0.0579 0.8552 29 G 0.1454 0.0545 0.8001 30 Q 0.3412 0.0397 0.6191 31 K 0.4649 0.0265 0.5086 32 Y 0.5861 0.0228 0.3911 33 K 0.7168 0.0143 0.2689 34 D 0.8267 0.0063 0.1670 35 Y 0.9176 0.0033 0.0790 36 E 0.9494 0.0025 0.0481 37 Y 0.9540 0.0025 0.0435 38 K 0.9470 0.0025 0.0505 39 L 0.8939 0.0030 0.1031 40 T 0.8778 0.0034 0.1188 41 G 0.8758 0.0047 0.1195 42 F 0.9167 0.0028 0.0805 43 D 0.4308 0.0116 0.5576 44 K 0.0273 0.0237 0.9489 45 D 0.0113 0.0170 0.9717 46 G 0.0376 0.0152 0.9473 47 K 0.3223 0.0049 0.6729 48 E 0.9064 0.0027 0.0908 49 K 0.9437 0.0026 0.0537 50 E 0.9632 0.0025 0.0343 51 L 0.9593 0.0025 0.0382 52 E 0.9626 0.0025 0.0349 53 F 0.9426 0.0025 0.0548 54 T 0.7051 0.0046 0.2903 55 A 0.2625 0.0284 0.7091 56 Q 0.0761 0.0539 0.8700 57 K 0.0615 0.0903 0.8482 58 N 0.0985 0.1201 0.7815 59 L 0.1546 0.1166 0.7288 60 R 0.1063 0.0561 0.8376 61 K 0.0670 0.1023 0.8307 62 E 0.0715 0.0618 0.8666 63 A 0.3968 0.0204 0.5828 64 F 0.8747 0.0055 0.1198 65 L 0.9568 0.0034 0.0398 66 R 0.9714 0.0030 0.0256 67 V 0.9668 0.0025 0.0307 68 Y 0.9573 0.0032 0.0395 69 H 0.9014 0.0051 0.0935 70 S 0.4229 0.0203 0.5568 71 D 0.0723 0.0437 0.8839 72 K 0.1520 0.0520 0.7960 73 K 0.2225 0.0343 0.7432 74 G 0.3387 0.0167 0.6447 75 V 0.7134 0.0065 0.2801 76 S 0.7770 0.0054 0.2177 77 A 0.6888 0.0122 0.2989 78 W 0.3512 0.2588 0.3899 79 E 0.4746 0.2562 0.2692 80 E 0.4971 0.2501 0.2528 81 V 0.3255 0.0662 0.6083 82 K 0.1948 0.0572 0.7480 83 K 0.0174 0.7418 0.2408 84 D 0.0148 0.6720 0.3132 85 E 0.0215 0.6354 0.3431 86 L 0.0544 0.2111 0.7345 87 P 0.0172 0.2364 0.7464 88 A 0.0039 0.9139 0.0822 89 K 0.0038 0.9403 0.0559 90 V 0.0038 0.9601 0.0361 91 K 0.0041 0.9564 0.0395 92 E 0.0052 0.9246 0.0702 93 K 0.0057 0.8599 0.1344 94 L 0.0155 0.6040 0.3804 95 G 0.0355 0.1735 0.7910 96 V 0.0614 0.0548 0.8838 97 K 0.0176 0.0128 0.9696