# This file is the result of combining several RDB files, specifically # T0353.t06.dssp-ebghstl.rdb (weight 1.53986) # T0353.t06.stride-ebghtl.rdb (weight 1.24869) # T0353.t06.str2.rdb (weight 1.54758) # T0353.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 T0353.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.stride-ebghtl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.str2.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ # Comments from T0353.t06.alpha.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37346 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1502 0.0078 0.8419 2 Q 0.7136 0.0055 0.2810 3 I 0.8662 0.0043 0.1295 4 H 0.8970 0.0052 0.0978 5 V 0.9002 0.0061 0.0938 6 Y 0.8637 0.0086 0.1278 7 D 0.7340 0.0107 0.2553 8 T 0.5740 0.0427 0.3833 9 Y 0.7873 0.0245 0.1881 10 V 0.8624 0.0143 0.1233 11 K 0.8294 0.0117 0.1588 12 A 0.6481 0.0211 0.3307 13 K 0.2140 0.0646 0.7215 14 D 0.0489 0.0296 0.9215 15 G 0.0725 0.0286 0.8989 16 H 0.4606 0.0130 0.5263 17 V 0.9128 0.0038 0.0834 18 M 0.9132 0.0044 0.0824 19 H 0.9218 0.0037 0.0745 20 F 0.8909 0.0050 0.1041 21 D 0.8639 0.0082 0.1279 22 V 0.8716 0.0098 0.1186 23 F 0.8644 0.0162 0.1194 24 T 0.7878 0.0230 0.1891 25 D 0.4775 0.0273 0.4952 26 V 0.1400 0.1857 0.6742 27 R 0.0674 0.2228 0.7097 28 D 0.0530 0.2233 0.7236 29 D 0.0236 0.6056 0.3708 30 K 0.0099 0.8703 0.1198 31 K 0.0125 0.9130 0.0745 32 A 0.0101 0.9323 0.0576 33 I 0.0049 0.9530 0.0420 34 E 0.0047 0.9558 0.0395 35 F 0.0047 0.9564 0.0390 36 A 0.0047 0.9563 0.0390 37 K 0.0047 0.9593 0.0360 38 Q 0.0048 0.9538 0.0414 39 W 0.0049 0.9425 0.0526 40 L 0.0060 0.9241 0.0699 41 S 0.0075 0.8691 0.1234 42 S 0.0121 0.7918 0.1960 43 I 0.0483 0.5443 0.4075 44 G 0.0656 0.1735 0.7609 45 E 0.1050 0.2027 0.6923 46 E 0.1141 0.1753 0.7105 47 G 0.0818 0.1147 0.8035 48 A 0.1469 0.0616 0.7915 49 T 0.3524 0.0430 0.6046 50 V 0.3439 0.0362 0.6198 51 T 0.2613 0.0440 0.6947 52 S 0.1325 0.2864 0.5811 53 E 0.0744 0.3940 0.5316 54 E 0.1210 0.3806 0.4985 55 C 0.2141 0.2299 0.5559 56 R 0.1763 0.2731 0.5506 57 F 0.2667 0.2742 0.4591 58 C 0.2340 0.2731 0.4928 59 H 0.1533 0.2669 0.5797 60 S 0.0612 0.4821 0.4567 61 Q 0.0407 0.4478 0.5115 62 K 0.0474 0.3250 0.6275 63 A 0.0692 0.0511 0.8797 64 P 0.0483 0.1025 0.8492 65 D 0.0055 0.9264 0.0682 66 E 0.0053 0.9434 0.0513 67 V 0.0051 0.9491 0.0459 68 I 0.0050 0.9578 0.0372 69 E 0.0049 0.9582 0.0369 70 A 0.0048 0.9568 0.0385 71 I 0.0048 0.9514 0.0438 72 K 0.0054 0.9338 0.0609 73 Q 0.0184 0.7591 0.2225 74 N 0.0435 0.1513 0.8051 75 G 0.0541 0.0273 0.9186 76 Y 0.3188 0.0103 0.6708 77 F 0.8596 0.0065 0.1339 78 I 0.9069 0.0102 0.0829 79 Y 0.8921 0.0132 0.0947 80 K 0.8652 0.0127 0.1222 81 M 0.6975 0.0295 0.2731 82 E 0.3655 0.0985 0.5360 83 G 0.1206 0.0657 0.8137 84 C 0.1361 0.0322 0.8317 85 N 0.0741 0.0405 0.8854