# This file is the result of combining several RDB files, specifically # T0386.t06.dssp-ebghstl.rdb (weight 1.53986) # T0386.t06.stride-ebghtl.rdb (weight 1.24869) # T0386.t06.str2.rdb (weight 1.54758) # T0386.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 T0386.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.stride-ebghtl.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.str2.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 3.39455 # # ============================================ # Comments from T0386.t06.alpha.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 3.39455 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0480 0.0211 0.9308 2 P 0.0632 0.0951 0.8417 3 K 0.0696 0.2467 0.6837 4 A 0.0766 0.3683 0.5551 5 K 0.0810 0.4241 0.4949 6 A 0.1057 0.3987 0.4956 7 K 0.1134 0.3225 0.5640 8 T 0.1652 0.1983 0.6365 9 K 0.1584 0.1812 0.6604 10 N 0.1813 0.1082 0.7105 11 T 0.2394 0.1276 0.6330 12 E 0.4431 0.0950 0.4619 13 I 0.5538 0.0659 0.3803 14 I 0.4505 0.0508 0.4987 15 S 0.2359 0.0315 0.7326 16 P 0.1029 0.1412 0.7559 17 H 0.1512 0.1598 0.6890 18 H 0.2530 0.1477 0.5993 19 Y 0.4233 0.0524 0.5243 20 V 0.6029 0.0308 0.3662 21 Y 0.2544 0.0184 0.7272 22 P 0.0508 0.0986 0.8506 23 N 0.0488 0.0606 0.8906 24 T 0.1467 0.1261 0.7272 25 T 0.2139 0.2302 0.5559 26 T 0.4173 0.2592 0.3235 27 L 0.4021 0.3043 0.2937 28 K 0.3627 0.3158 0.3215 29 N 0.2547 0.2724 0.4729 30 K 0.1119 0.4332 0.4549 31 Y 0.1146 0.2571 0.6283 32 G 0.1131 0.1805 0.7064 33 I 0.1716 0.2351 0.5933 34 K 0.1803 0.2471 0.5726 35 N 0.1547 0.1651 0.6802 36 L 0.0065 0.9109 0.0827 37 N 0.0055 0.9334 0.0612 38 A 0.0056 0.9328 0.0616 39 F 0.0058 0.9344 0.0598 40 L 0.0067 0.9306 0.0627 41 E 0.0079 0.9074 0.0847 42 K 0.0107 0.8563 0.1331 43 C 0.0348 0.6781 0.2871 44 S 0.0319 0.5243 0.4438 45 H 0.0358 0.4544 0.5098 46 D 0.0355 0.5866 0.3779 47 T 0.0219 0.6873 0.2908 48 A 0.0201 0.8176 0.1623 49 K 0.0354 0.8009 0.1636 50 A 0.0744 0.7678 0.1578 51 M 0.1303 0.7207 0.1490 52 I 0.1709 0.6362 0.1930 53 N 0.1830 0.5119 0.3051 54 L 0.1092 0.4879 0.4029 55 R 0.0920 0.3919 0.5161 56 E 0.0893 0.3758 0.5349 57 E 0.0790 0.2244 0.6966 58 S 0.0759 0.1909 0.7332 59 L 0.0630 0.1023 0.8347 60 P 0.0454 0.3737 0.5810 61 E 0.0251 0.5018 0.4732 62 Y 0.0367 0.5704 0.3930 63 F 0.0883 0.3615 0.5502 64 D 0.0568 0.4275 0.5157 65 T 0.0533 0.7731 0.1736 66 A 0.0432 0.8670 0.0899 67 Y 0.0395 0.8912 0.0693 68 L 0.0311 0.9049 0.0640 69 C 0.0209 0.9184 0.0608 70 H 0.0187 0.9190 0.0623 71 I 0.0168 0.9094 0.0739 72 H 0.0196 0.8921 0.0883 73 Q 0.0205 0.8261 0.1534 74 Q 0.0193 0.6672 0.3135 75 L 0.0274 0.1291 0.8435