# This file is the result of combining several RDB files, specifically # T0295.t06.dssp-ebghstl.rdb (weight 1.53986) # T0295.t06.stride-ebghtl.rdb (weight 1.24869) # T0295.t06.str2.rdb (weight 1.54758) # T0295.t06.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.t06.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.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 10.6155 # # ============================================ # Comments from T0295.t06.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.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 10.6155 # # ============================================ # Comments from T0295.t06.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.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 10.6155 # # ============================================ # Comments from T0295.t06.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.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 10.6155 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0726 0.0298 0.8976 2 S 0.0863 0.0485 0.8651 3 F 0.0952 0.0554 0.8494 4 L 0.0983 0.0569 0.8448 5 T 0.0667 0.0595 0.8738 6 N 0.0821 0.0670 0.8509 7 F 0.0207 0.5885 0.3908 8 D 0.0150 0.6971 0.2879 9 E 0.0261 0.8105 0.1634 10 W 0.0191 0.8499 0.1310 11 D 0.0091 0.8889 0.1020 12 N 0.0076 0.9282 0.0643 13 L 0.0092 0.9391 0.0517 14 L 0.0130 0.9424 0.0446 15 R 0.0150 0.9475 0.0375 16 I 0.0128 0.9481 0.0392 17 C 0.0150 0.9322 0.0528 18 F 0.0338 0.8712 0.0950 19 S 0.0546 0.7932 0.1522 20 R 0.0474 0.6777 0.2749 21 K 0.0403 0.6197 0.3400 22 R 0.0757 0.4076 0.5167 23 K 0.1704 0.2556 0.5740 24 T 0.3567 0.2674 0.3759 25 L 0.2729 0.4559 0.2712 26 H 0.2447 0.4913 0.2639 27 A 0.2779 0.4915 0.2306 28 I 0.2201 0.5556 0.2244 29 F 0.1706 0.4854 0.3439 30 K 0.1025 0.4510 0.4466 31 R 0.0494 0.6548 0.2958 32 N 0.0158 0.8263 0.1579 33 A 0.0204 0.8613 0.1182 34 V 0.0092 0.9402 0.0507 35 L 0.0057 0.9548 0.0395 36 N 0.0050 0.9572 0.0378 37 M 0.0052 0.9536 0.0412 38 L 0.0056 0.9410 0.0534 39 E 0.0065 0.9217 0.0718 40 H 0.0170 0.7699 0.2131 41 N 0.0285 0.4822 0.4893 42 Y 0.0670 0.4908 0.4422 43 K 0.1702 0.4513 0.3785 44 N 0.2861 0.4316 0.2823 45 W 0.3062 0.4706 0.2232 46 C 0.3210 0.3889 0.2901 47 T 0.3362 0.2936 0.3702 48 L 0.2234 0.2395 0.5371 49 N 0.1511 0.1699 0.6790 50 K 0.1384 0.0962 0.7654 51 Q 0.2920 0.0697 0.6383 52 V 0.2751 0.0265 0.6984 53 P 0.1340 0.0398 0.8262 54 V 0.0741 0.1001 0.8258 55 N 0.0635 0.0769 0.8596 56 F 0.0664 0.1101 0.8235 57 P 0.0662 0.2728 0.6610 58 F 0.0200 0.8395 0.1406 59 K 0.0084 0.9153 0.0764 60 K 0.0062 0.9503 0.0435 61 Y 0.0070 0.9458 0.0472 62 C 0.0055 0.9548 0.0397 63 L 0.0047 0.9596 0.0357 64 D 0.0047 0.9563 0.0390 65 V 0.0047 0.9557 0.0396 66 L 0.0048 0.9437 0.0515 67 E 0.0053 0.8859 0.1088 68 H 0.0086 0.7653 0.2261 69 L 0.0494 0.5257 0.4250 70 D 0.0262 0.4406 0.5332 71 M 0.0147 0.6780 0.3073 72 C 0.0270 0.7029 0.2701 73 E 0.0351 0.7171 0.2477 74 K 0.0360 0.6861 0.2780 75 R 0.0482 0.5967 0.3552 76 S 0.0659 0.5806 0.3536 77 I 0.0714 0.5083 0.4203 78 N 0.1047 0.2651 0.6302 79 L 0.1277 0.1155 0.7568 80 D 0.0770 0.0759 0.8471 81 E 0.0050 0.9187 0.0763 82 N 0.0048 0.9420 0.0532 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 0.0063 0.9138 0.0800 92 N 0.0120 0.7974 0.1906 93 K 0.0151 0.6903 0.2946 94 K 0.0425 0.2620 0.6955 95 G 0.0714 0.0694 0.8592 96 I 0.4413 0.0227 0.5360 97 H 0.7598 0.0159 0.2243 98 F 0.7071 0.0164 0.2765 99 F 0.4150 0.0267 0.5583