# This file is the result of combining several RDB files, specifically # T0206.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0206.t2k.stride-ebghtl.rdb (weight 1.24869) # T0206.t2k.str2.rdb (weight 1.54758) # T0206.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 T0206.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0206 # 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 T0206.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 72 # # ============================================ # Comments from T0206.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0206 # 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 T0206.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 72 # # ============================================ # Comments from T0206.t2k.str2.rdb # ============================================ # TARGET T0206 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0206.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 72 # # ============================================ # Comments from T0206.t2k.alpha.rdb # ============================================ # TARGET T0206 # 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 T0206.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 72 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1056 0.0314 0.8630 2 A 0.2095 0.0360 0.7546 3 F 0.2229 0.0606 0.7164 4 D 0.1367 0.0706 0.7927 5 P 0.0395 0.3481 0.6124 6 N 0.0486 0.3166 0.6348 7 L 0.0782 0.3403 0.5815 8 V 0.1419 0.1981 0.6600 9 G 0.0883 0.1753 0.7364 10 P 0.0774 0.1985 0.7241 11 T 0.1466 0.1686 0.6848 12 L 0.1701 0.0715 0.7584 13 P 0.1309 0.0552 0.8139 14 P 0.1592 0.1095 0.7312 15 I 0.1913 0.0831 0.7256 16 P 0.1493 0.0800 0.7707 17 P 0.1484 0.1129 0.7386 18 F 0.2223 0.0948 0.6829 19 T 0.2268 0.0709 0.7023 20 L 0.1373 0.0411 0.8216 21 P 0.1278 0.0583 0.8140 22 T 0.1948 0.0559 0.7492 23 G 0.1079 0.0370 0.8551 24 P 0.1037 0.0541 0.8422 25 T 0.1277 0.0570 0.8153 26 G 0.0907 0.0405 0.8688 27 P 0.1049 0.0636 0.8314 28 T 0.1587 0.0629 0.7785 29 G 0.1084 0.0490 0.8426 30 P 0.1016 0.0749 0.8235 31 T 0.1692 0.0731 0.7576 32 G 0.1120 0.0497 0.8383 33 P 0.0960 0.0702 0.8338 34 T 0.1206 0.0675 0.8119 35 G 0.0923 0.0493 0.8583 36 P 0.1097 0.0663 0.8239 37 T 0.1721 0.0617 0.7662 38 G 0.1072 0.0481 0.8447 39 P 0.1110 0.0637 0.8253 40 T 0.1832 0.0647 0.7521 41 G 0.1130 0.0585 0.8285 42 P 0.1086 0.0779 0.8135 43 T 0.1456 0.0663 0.7882 44 G 0.1133 0.0548 0.8318 45 D 0.1020 0.0753 0.8226 46 T 0.1325 0.0741 0.7934 47 G 0.1079 0.0571 0.8349 48 T 0.1131 0.0747 0.8122 49 T 0.1701 0.0712 0.7587 50 G 0.1170 0.0491 0.8340 51 P 0.1103 0.0685 0.8213 52 T 0.1559 0.0668 0.7774 53 G 0.1154 0.0523 0.8323 54 P 0.0953 0.0793 0.8254 55 T 0.1127 0.0655 0.8218 56 G 0.0917 0.0480 0.8604 57 P 0.0999 0.0694 0.8307 58 T 0.1687 0.0666 0.7647 59 G 0.1037 0.0580 0.8383 60 P 0.0984 0.0772 0.8243 61 T 0.1433 0.0694 0.7873 62 G 0.1117 0.0579 0.8303 63 P 0.1060 0.0833 0.8107 64 T 0.1305 0.0829 0.7867 65 G 0.1171 0.0702 0.8127 66 A 0.1200 0.0893 0.7907 67 T 0.1478 0.0845 0.7676 68 G 0.1108 0.0597 0.8295 69 L 0.1005 0.0865 0.8130 70 T 0.1225 0.0769 0.8006 71 G 0.0952 0.0577 0.8471 72 P 0.0903 0.0771 0.8327 73 T 0.1104 0.0688 0.8207 74 G 0.0805 0.0463 0.8732 75 P 0.1119 0.0628 0.8253 76 T 0.1960 0.0642 0.7398 77 G 0.1086 0.0535 0.8379 78 P 0.0994 0.0815 0.8191 79 S 0.1235 0.0775 0.7990 80 G 0.0986 0.0730 0.8284 81 L 0.0876 0.1032 0.8092 82 G 0.0935 0.1047 0.8018 83 L 0.0806 0.0851 0.8343 84 P 0.0858 0.3178 0.5964 85 A 0.1114 0.3635 0.5251 86 G 0.1610 0.3939 0.4451 87 L 0.2536 0.3824 0.3640 88 Y 0.3056 0.2669 0.4275 89 A 0.2630 0.1918 0.5452 90 F 0.0558 0.0434 0.9008