# This file is the result of combining several RDB files, specifically # T0295.t04.dssp-ebghstl.rdb (weight 1.53986) # T0295.t04.stride-ebghtl.rdb (weight 1.24869) # T0295.t04.str2.rdb (weight 1.54758) # T0295.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 T0295.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 10.7648 # # ============================================ # Comments from T0295.t04.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 10.7648 # # ============================================ # Comments from T0295.t04.str2.rdb # ============================================ # TARGET T0295 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0295.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 10.7648 # # ============================================ # Comments from T0295.t04.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 10.7648 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0707 0.0285 0.9007 2 S 0.0869 0.0472 0.8659 3 F 0.0966 0.0583 0.8451 4 L 0.0997 0.0603 0.8400 5 T 0.0669 0.0613 0.8718 6 N 0.0824 0.0696 0.8480 7 F 0.0208 0.5986 0.3806 8 D 0.0148 0.7049 0.2803 9 E 0.0238 0.8168 0.1594 10 W 0.0182 0.8546 0.1272 11 D 0.0089 0.8926 0.0985 12 N 0.0073 0.9298 0.0629 13 L 0.0090 0.9401 0.0510 14 L 0.0130 0.9427 0.0444 15 R 0.0148 0.9478 0.0375 16 I 0.0125 0.9483 0.0392 17 C 0.0148 0.9323 0.0529 18 F 0.0334 0.8722 0.0945 19 S 0.0541 0.7950 0.1509 20 R 0.0469 0.6803 0.2728 21 K 0.0398 0.6225 0.3377 22 R 0.0754 0.4108 0.5138 23 K 0.1691 0.2586 0.5723 24 T 0.3527 0.2714 0.3759 25 L 0.2680 0.4620 0.2700 26 H 0.2408 0.4963 0.2630 27 A 0.2735 0.4961 0.2304 28 I 0.2167 0.5593 0.2240 29 F 0.1685 0.4887 0.3429 30 K 0.1012 0.4546 0.4443 31 R 0.0495 0.6550 0.2955 32 N 0.0158 0.8273 0.1570 33 A 0.0205 0.8616 0.1180 34 V 0.0092 0.9402 0.0507 35 L 0.0054 0.9550 0.0395 36 N 0.0050 0.9572 0.0378 37 M 0.0052 0.9536 0.0412 38 L 0.0056 0.9414 0.0531 39 E 0.0065 0.9217 0.0718 40 H 0.0168 0.7707 0.2125 41 N 0.0284 0.4829 0.4886 42 Y 0.0666 0.4924 0.4410 43 K 0.1696 0.4530 0.3774 44 N 0.2849 0.4335 0.2816 45 W 0.3048 0.4728 0.2224 46 C 0.3200 0.3908 0.2892 47 T 0.3351 0.2953 0.3697 48 L 0.2227 0.2404 0.5368 49 N 0.1512 0.1705 0.6784 50 K 0.1381 0.0969 0.7650 51 Q 0.2908 0.0701 0.6391 52 V 0.2742 0.0268 0.6990 53 P 0.1331 0.0399 0.8270 54 V 0.0733 0.1000 0.8267 55 N 0.0624 0.0768 0.8608 56 F 0.0663 0.1113 0.8223 57 P 0.0661 0.2767 0.6572 58 F 0.0199 0.8403 0.1398 59 K 0.0083 0.9160 0.0757 60 K 0.0062 0.9503 0.0435 61 Y 0.0070 0.9464 0.0466 62 C 0.0055 0.9548 0.0397 63 L 0.0047 0.9596 0.0357 64 D 0.0047 0.9567 0.0386 65 V 0.0047 0.9557 0.0396 66 L 0.0048 0.9437 0.0515 67 E 0.0053 0.8862 0.1085 68 H 0.0086 0.7656 0.2258 69 L 0.0494 0.5252 0.4255 70 D 0.0263 0.4400 0.5337 71 M 0.0147 0.6785 0.3068 72 C 0.0270 0.7036 0.2694 73 E 0.0351 0.7181 0.2468 74 K 0.0359 0.6862 0.2778 75 R 0.0481 0.5966 0.3553 76 S 0.0655 0.5813 0.3532 77 I 0.0706 0.5092 0.4201 78 N 0.1039 0.2660 0.6301 79 L 0.1274 0.1155 0.7571 80 D 0.0770 0.0762 0.8467 81 E 0.0050 0.9187 0.0763 82 N 0.0048 0.9421 0.0531 83 D 0.0049 0.9507 0.0444 84 F 0.0047 0.9596 0.0357 85 L 0.0047 0.9606 0.0347 86 K 0.0046 0.9616 0.0338 87 L 0.0047 0.9599 0.0355 88 L 0.0047 0.9573 0.0380 89 L 0.0048 0.9534 0.0419 90 E 0.0049 0.9462 0.0489 91 F 0.0062 0.9139 0.0799 92 N 0.0120 0.7974 0.1907 93 K 0.0151 0.6904 0.2945 94 K 0.0425 0.2615 0.6961 95 G 0.0714 0.0694 0.8593 96 I 0.4416 0.0227 0.5357 97 H 0.7603 0.0159 0.2237 98 F 0.7072 0.0163 0.2765 99 F 0.4155 0.0267 0.5577