# This file is the result of combining several RDB files, specifically # T0340.t04.dssp-ebghstl.rdb (weight 1.53986) # T0340.t04.stride-ebghtl.rdb (weight 1.24869) # T0340.t04.str2.rdb (weight 1.54758) # T0340.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 T0340.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.stride-ebghtl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.str2.rdb # ============================================ # TARGET T0340 # Using neural net t04-2621-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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.alpha.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0706 0.0405 0.8889 2 M 0.0951 0.0601 0.8449 3 L 0.1287 0.0470 0.8243 4 R 0.2104 0.0157 0.7739 5 P 0.3975 0.0087 0.5939 6 R 0.7798 0.0061 0.2141 7 L 0.9017 0.0033 0.0950 8 C 0.9070 0.0038 0.0893 9 H 0.9215 0.0033 0.0752 10 L 0.8986 0.0040 0.0974 11 R 0.8033 0.0055 0.1912 12 K 0.5964 0.0278 0.3758 13 G 0.2321 0.0176 0.7503 14 P 0.0842 0.0616 0.8542 15 Q 0.0757 0.0637 0.8606 16 G 0.2025 0.0539 0.7435 17 Y 0.4050 0.0284 0.5666 18 G 0.7848 0.0104 0.2048 19 F 0.8869 0.0044 0.1087 20 N 0.9098 0.0038 0.0863 21 L 0.9006 0.0044 0.0950 22 H 0.7926 0.0153 0.1921 23 S 0.5319 0.0261 0.4420 24 D 0.2459 0.0435 0.7106 25 K 0.1840 0.0685 0.7475 26 S 0.1592 0.0581 0.7828 27 R 0.1224 0.0373 0.8403 28 P 0.1010 0.0548 0.8442 29 G 0.2730 0.0372 0.6898 30 Q 0.7083 0.0083 0.2834 31 Y 0.8863 0.0047 0.1090 32 I 0.8954 0.0031 0.1015 33 R 0.8249 0.0302 0.1449 34 S 0.7568 0.0064 0.2368 35 V 0.5439 0.0099 0.4462 36 D 0.1598 0.0169 0.8233 37 P 0.0286 0.0790 0.8924 38 G 0.0244 0.0438 0.9318 39 S 0.0789 0.0448 0.8763 40 P 0.0374 0.7741 0.1884 41 A 0.0189 0.8423 0.1388 42 A 0.0146 0.8494 0.1360 43 R 0.0197 0.8137 0.1665 44 S 0.0495 0.3637 0.5867 45 G 0.0443 0.1045 0.8512 46 L 0.1029 0.0197 0.8774 47 R 0.1282 0.0218 0.8499 48 A 0.0699 0.1862 0.7440 49 Q 0.0894 0.1055 0.8051 50 D 0.2946 0.0621 0.6433 51 R 0.7892 0.0133 0.1975 52 L 0.9148 0.0062 0.0790 53 I 0.9088 0.0078 0.0834 54 E 0.9071 0.0034 0.0895 55 V 0.8187 0.0174 0.1639 56 N 0.3519 0.0186 0.6295 57 G 0.1816 0.0304 0.7879 58 Q 0.5659 0.0150 0.4191 59 N 0.6631 0.0134 0.3236 60 V 0.3021 0.1133 0.5846 61 E 0.0862 0.1259 0.7879 62 G 0.0542 0.0785 0.8673 63 L 0.1779 0.0205 0.8015 64 R 0.1805 0.0202 0.7993 65 H 0.0054 0.9427 0.0519 66 A 0.0047 0.9604 0.0350 67 E 0.0047 0.9608 0.0345 68 V 0.0047 0.9608 0.0345 69 V 0.0047 0.9606 0.0347 70 A 0.0046 0.9600 0.0353 71 S 0.0050 0.9551 0.0399 72 I 0.0064 0.9373 0.0564 73 K 0.0079 0.8748 0.1173 74 A 0.0141 0.5947 0.3913 75 R 0.0539 0.1466 0.7996 76 E 0.0382 0.0834 0.8784 77 D 0.0710 0.0568 0.8722 78 E 0.5096 0.0169 0.4735 79 A 0.8681 0.0041 0.1278 80 R 0.9200 0.0034 0.0766 81 L 0.9305 0.0032 0.0663 82 L 0.9244 0.0036 0.0719 83 V 0.9196 0.0033 0.0771 84 V 0.7669 0.0150 0.2182 85 G 0.3223 0.0119 0.6657 86 P 0.0752 0.0541 0.8707 87 S 0.0671 0.0398 0.8931 88 T 0.0732 0.0481 0.8787 89 R 0.0776 0.0362 0.8862 90 L 0.0660 0.0397 0.8943