# This file is the result of combining several RDB files, specifically # YGR018C.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR018C.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR018C.t2k.str2.rdb (weight 1.54758) # YGR018C.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 YGR018C.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR018C # 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 YGR018C.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 1 # # ============================================ # Comments from YGR018C.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR018C # 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 YGR018C.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 1 # # ============================================ # Comments from YGR018C.t2k.str2.rdb # ============================================ # TARGET YGR018C # 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 YGR018C.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 1 # # ============================================ # Comments from YGR018C.t2k.alpha.rdb # ============================================ # TARGET YGR018C # 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 YGR018C.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0926 0.0360 0.8714 2 I 0.2576 0.0573 0.6851 3 D 0.3585 0.0611 0.5804 4 I 0.2753 0.1405 0.5842 5 S 0.2242 0.1376 0.6382 6 H 0.1481 0.1418 0.7101 7 G 0.1077 0.1048 0.7875 8 H 0.1850 0.1042 0.7108 9 T 0.2510 0.1306 0.6184 10 S 0.2266 0.1507 0.6227 11 C 0.1881 0.1733 0.6386 12 S 0.1471 0.2057 0.6472 13 S 0.1165 0.2418 0.6417 14 H 0.1217 0.2377 0.6406 15 R 0.1201 0.2388 0.6411 16 S 0.0963 0.2722 0.6315 17 S 0.0691 0.2857 0.6452 18 S 0.0836 0.2427 0.6737 19 L 0.1127 0.2025 0.6848 20 P 0.1140 0.3140 0.5720 21 S 0.2032 0.3815 0.4152 22 V 0.3409 0.3803 0.2788 23 F 0.4745 0.2982 0.2273 24 W 0.5108 0.2689 0.2203 25 K 0.5513 0.2401 0.2086 26 I 0.5240 0.2132 0.2629 27 H 0.4465 0.1592 0.3943 28 L 0.2864 0.1118 0.6018 29 S 0.1439 0.0560 0.8001 30 P 0.0981 0.0853 0.8166 31 P 0.1022 0.0929 0.8049 32 L 0.1132 0.1164 0.7704 33 P 0.1060 0.1875 0.7065 34 S 0.1373 0.2299 0.6328 35 F 0.2597 0.2178 0.5226 36 K 0.3445 0.1881 0.4673 37 F 0.3370 0.1939 0.4691 38 K 0.2639 0.1983 0.5378 39 K 0.2003 0.2172 0.5825 40 S 0.1641 0.1894 0.6466 41 T 0.1438 0.2071 0.6491 42 E 0.1342 0.2783 0.5875 43 S 0.1402 0.3006 0.5592 44 T 0.1608 0.2897 0.5495 45 Q 0.1814 0.2986 0.5201 46 R 0.2024 0.3170 0.4806 47 Q 0.2187 0.2843 0.4971 48 T 0.2470 0.2453 0.5077 49 I 0.2147 0.1909 0.5944 50 P 0.1483 0.1967 0.6550 51 K 0.1453 0.2510 0.6036 52 F 0.1510 0.2118 0.6371 53 S 0.1253 0.1574 0.7173 54 S 0.1027 0.1398 0.7575 55 P 0.0762 0.2980 0.6258 56 A 0.0595 0.4486 0.4919 57 S 0.0524 0.4659 0.4817 58 S 0.0756 0.3745 0.5499 59 L 0.1133 0.2391 0.6476 60 A 0.0963 0.1186 0.7851 61 P 0.0776 0.1490 0.7734 62 S 0.0829 0.1584 0.7587 63 T 0.1100 0.1055 0.7846 64 P 0.1739 0.1580 0.6681 65 L 0.2456 0.2530 0.5013 66 W 0.3134 0.2444 0.4422 67 S 0.3247 0.2177 0.4576 68 L 0.2365 0.3121 0.4514 69 S 0.2092 0.3147 0.4761 70 S 0.2615 0.2876 0.4509 71 C 0.4787 0.1766 0.3447 72 L 0.6530 0.1062 0.2408 73 L 0.7361 0.0775 0.1864 74 V 0.6838 0.0865 0.2298 75 S 0.6117 0.0995 0.2888 76 E 0.5767 0.1133 0.3100 77 V 0.6039 0.0879 0.3082 78 S 0.5854 0.0946 0.3200 79 F 0.5155 0.0986 0.3859 80 W 0.3423 0.0765 0.5812 81 P 0.1112 0.1717 0.7171 82 G 0.0813 0.1644 0.7543 83 A 0.1196 0.2194 0.6610 84 G 0.1960 0.2027 0.6012 85 F 0.4136 0.1919 0.3946 86 L 0.4912 0.1765 0.3323 87 Y 0.4049 0.2117 0.3834 88 N 0.2824 0.1865 0.5312 89 D 0.2835 0.1853 0.5312 90 L 0.5507 0.1192 0.3301 91 V 0.6940 0.0732 0.2328 92 C 0.6909 0.0617 0.2474 93 L 0.5199 0.0809 0.3992 94 D 0.2972 0.0766 0.6262 95 R 0.1045 0.2791 0.6164 96 E 0.0718 0.3534 0.5748 97 D 0.0818 0.3910 0.5272 98 H 0.1306 0.3275 0.5418 99 C 0.2061 0.2768 0.5170 100 L 0.1839 0.2840 0.5320 101 S 0.1221 0.2861 0.5918 102 N 0.0876 0.2740 0.6385 103 S 0.0880 0.2883 0.6237 104 A 0.0942 0.3328 0.5729 105 S 0.0970 0.3451 0.5579 106 H 0.1050 0.3069 0.5881 107 S 0.1143 0.2282 0.6576 108 C 0.0902 0.1440 0.7658 109 G 0.0388 0.0420 0.9192