# This file is the result of combining several RDB files, specifically # T0170.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0170.t2k.stride-ebghtl.rdb (weight 1.24869) # T0170.t2k.str.rdb (weight 1.53983) # T0170.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 T0170.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0170 # 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 T0170.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 30 # # ============================================ # Comments from T0170.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0170 # 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 T0170.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 30 # # ============================================ # Comments from T0170.t2k.str.rdb # ============================================ # TARGET T0170 # 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 T0170.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 30 # # ============================================ # Comments from T0170.t2k.alpha.rdb # ============================================ # TARGET T0170 # 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 T0170.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 30 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Q 0.0365 0.1023 0.8612 2 P 0.0436 0.3531 0.6033 3 A 0.0216 0.5686 0.4098 4 K 0.0147 0.6975 0.2878 5 K 0.0144 0.7272 0.2585 6 T 0.0153 0.7163 0.2684 7 Y 0.0172 0.6924 0.2904 8 T 0.0256 0.6783 0.2961 9 W 0.0248 0.6040 0.3711 10 N 0.0347 0.5183 0.4470 11 T 0.0185 0.5955 0.3861 12 K 0.0056 0.8977 0.0967 13 E 0.0056 0.9301 0.0643 14 E 0.0051 0.9400 0.0549 15 A 0.0056 0.9339 0.0605 16 K 0.0056 0.9485 0.0459 17 Q 0.0060 0.9469 0.0471 18 A 0.0062 0.9432 0.0506 19 F 0.0051 0.9429 0.0520 20 K 0.0046 0.9527 0.0428 21 E 0.0046 0.9483 0.0471 22 L 0.0048 0.9400 0.0552 23 L 0.0078 0.9208 0.0713 24 K 0.0061 0.8723 0.1216 25 E 0.0112 0.7304 0.2584 26 K 0.0481 0.3727 0.5791 27 R 0.0461 0.0616 0.8923 28 V 0.1193 0.0189 0.8618 29 P 0.0720 0.0258 0.9022 30 S 0.0177 0.1302 0.8521 31 N 0.0224 0.0699 0.9077 32 A 0.1235 0.0419 0.8346 33 S 0.1416 0.0939 0.7645 34 W 0.0120 0.8769 0.1112 35 E 0.0080 0.8995 0.0925 36 Q 0.0074 0.9132 0.0794 37 A 0.0094 0.9024 0.0882 38 M 0.0114 0.9111 0.0775 39 K 0.0065 0.9172 0.0763 40 M 0.0091 0.9065 0.0844 41 I 0.0196 0.8645 0.1159 42 I 0.0223 0.7222 0.2555 43 N 0.0243 0.4545 0.5212 44 D 0.0686 0.1050 0.8264 45 P 0.0177 0.3865 0.5958 46 R 0.0321 0.4442 0.5237 47 Y 0.0867 0.5115 0.4018 48 S 0.1611 0.5081 0.3308 49 A 0.1703 0.4494 0.3804 50 L 0.1477 0.3402 0.5120 51 A 0.0724 0.2093 0.7183 52 N 0.0737 0.1024 0.8240 53 L 0.0275 0.6943 0.2782 54 S 0.0110 0.8267 0.1623 55 E 0.0095 0.8812 0.1093 56 K 0.0069 0.9177 0.0754 57 K 0.0055 0.9311 0.0635 58 Q 0.0057 0.9330 0.0613 59 A 0.0051 0.9353 0.0596 60 F 0.0047 0.9466 0.0487 61 N 0.0049 0.9492 0.0459 62 A 0.0048 0.9472 0.0480 63 Y 0.0053 0.9399 0.0547 64 K 0.0093 0.9228 0.0679 65 V 0.0131 0.8880 0.0989 66 Q 0.0210 0.8041 0.1749 67 T 0.0540 0.6157 0.3303 68 E 0.0657 0.3119 0.6224 69 K 0.0323 0.0614 0.9063