# This file is the result of combining several RDB files, specifically # T0379.t06.dssp-ebghstl.rdb (weight 1.53986) # T0379.t06.stride-ebghtl.rdb (weight 1.24869) # T0379.t06.str2.rdb (weight 1.54758) # T0379.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 T0379.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t06.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0694 0.1534 0.7772 2 L 0.0974 0.1718 0.7308 3 N 0.0836 0.1472 0.7692 4 R 0.0415 0.4859 0.4726 5 E 0.0272 0.7389 0.2339 6 E 0.0330 0.7525 0.2145 7 S 0.0556 0.7494 0.1949 8 I 0.0749 0.7709 0.1542 9 R 0.0949 0.7494 0.1557 10 R 0.1051 0.7209 0.1740 11 F 0.1420 0.6549 0.2031 12 K 0.1569 0.5833 0.2598 13 A 0.1972 0.5471 0.2557 14 I 0.1972 0.3240 0.4788 15 G 0.1873 0.1136 0.6991 16 V 0.2000 0.2878 0.5122 17 A 0.2341 0.2944 0.4715 18 D 0.2267 0.2827 0.4906 19 I 0.0119 0.8833 0.1048 20 E 0.0081 0.9115 0.0804 21 E 0.0097 0.8815 0.1087 22 M 0.0158 0.8014 0.1828 23 L 0.0346 0.6175 0.3479 24 D 0.0494 0.4456 0.5050 25 P 0.0067 0.7657 0.2276 26 Y 0.0119 0.7404 0.2476 27 L 0.0313 0.7315 0.2372 28 Q 0.0364 0.6703 0.2933 29 K 0.0484 0.4113 0.5402 30 G 0.0689 0.1830 0.7480 31 L 0.2381 0.1582 0.6036 32 F 0.5296 0.1271 0.3434 33 L 0.5690 0.1071 0.3239 34 D 0.4870 0.0855 0.4276 35 L 0.1623 0.3637 0.4741 36 E 0.0960 0.3322 0.5718 37 S 0.0748 0.2305 0.6947 38 G 0.0634 0.1139 0.8227 39 R 0.1241 0.1114 0.7644 40 K 0.1599 0.1385 0.7016 41 S 0.1029 0.1625 0.7346 42 E 0.0227 0.7950 0.1823 43 E 0.0146 0.8870 0.0984 44 E 0.0157 0.8983 0.0860 45 F 0.0195 0.8880 0.0924 46 R 0.0229 0.8833 0.0938 47 T 0.0193 0.8891 0.0916 48 E 0.0178 0.8891 0.0930 49 L 0.0211 0.8806 0.0983 50 S 0.0303 0.8375 0.1322 51 R 0.0362 0.8049 0.1589 52 Y 0.0497 0.7459 0.2044 53 I 0.0741 0.5871 0.3388 54 G 0.0696 0.3300 0.6005 55 K 0.0995 0.3830 0.5175 56 E 0.1891 0.4082 0.4026 57 L 0.1989 0.4032 0.3979 58 T 0.2001 0.4011 0.3988 59 Y 0.0663 0.7946 0.1392 60 Q 0.0341 0.8771 0.0889 61 Q 0.0399 0.8819 0.0781 62 V 0.0232 0.9092 0.0676 63 Y 0.0146 0.9269 0.0585 64 D 0.0122 0.9272 0.0606 65 A 0.0124 0.9229 0.0646 66 L 0.0122 0.9143 0.0735 67 L 0.0231 0.8569 0.1200 68 G 0.0311 0.7358 0.2331 69 F 0.0437 0.6774 0.2789 70 L 0.1038 0.4995 0.3966 71 E 0.0944 0.3378 0.5678 72 E 0.0404 0.1028 0.8568