# This file is the result of combining several RDB files, specifically # T0471.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0471.t2k.stride-ebghtl.rdb (weight 1.24869) # T0471.t2k.str2.rdb (weight 1.54758) # T0471.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 T0471.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ # Comments from T0471.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ # Comments from T0471.t2k.str2.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ # Comments from T0471.t2k.alpha.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0494 0.1030 0.8475 2 W 0.0780 0.2800 0.6420 3 N 0.0766 0.3922 0.5311 4 D 0.0286 0.7656 0.2057 5 L 0.0231 0.8426 0.1343 6 A 0.0374 0.8379 0.1247 7 V 0.0679 0.8236 0.1085 8 Y 0.1025 0.7871 0.1104 9 I 0.1204 0.7764 0.1032 10 I 0.1315 0.7644 0.1040 11 R 0.1429 0.7346 0.1225 12 C 0.1527 0.6563 0.1910 13 S 0.1612 0.4128 0.4259 14 G 0.0960 0.1278 0.7762 15 P 0.0535 0.0937 0.8528 16 G 0.0786 0.0667 0.8547 17 T 0.2807 0.0309 0.6884 18 R 0.6458 0.0092 0.3450 19 V 0.8952 0.0037 0.1011 20 V 0.9062 0.0050 0.0888 21 E 0.9132 0.0044 0.0824 22 V 0.8371 0.0143 0.1486 23 G 0.6993 0.0213 0.2794 24 A 0.4123 0.0496 0.5381 25 G 0.1737 0.0575 0.7688 26 R 0.1365 0.0963 0.7671 27 F 0.1134 0.1493 0.7373 28 L 0.0370 0.7031 0.2599 29 Y 0.0184 0.8291 0.1524 30 V 0.0057 0.9345 0.0598 31 S 0.0050 0.9506 0.0444 32 D 0.0049 0.9528 0.0423 33 Y 0.0049 0.9524 0.0427 34 I 0.0053 0.9497 0.0450 35 R 0.0053 0.9320 0.0627 36 K 0.0076 0.8556 0.1368 37 H 0.0436 0.3778 0.5786 38 S 0.0405 0.0271 0.9323 39 K 0.0958 0.0157 0.8886 40 V 0.5454 0.0111 0.4435 41 D 0.8407 0.0069 0.1524 42 L 0.9063 0.0047 0.0890 43 V 0.9063 0.0044 0.0893 44 L 0.8566 0.0095 0.1339 45 T 0.7287 0.0102 0.2611 46 D 0.5133 0.0408 0.4460 47 I 0.3599 0.0464 0.5937 48 K 0.1698 0.0657 0.7644 49 P 0.0844 0.0992 0.8165 50 S 0.0672 0.1035 0.8293 51 H 0.0956 0.0704 0.8340 52 G 0.2479 0.0311 0.7210 53 G 0.4256 0.0465 0.5279 54 I 0.6953 0.0370 0.2677 55 V 0.7278 0.0453 0.2268 56 R 0.6828 0.0792 0.2381 57 D 0.4613 0.1215 0.4172 58 D 0.2133 0.1957 0.5910 59 I 0.1443 0.2169 0.6388 60 T 0.1186 0.1555 0.7259 61 S 0.0878 0.0526 0.8596 62 P 0.0538 0.1429 0.8033 63 R 0.0900 0.1529 0.7570 64 M 0.0381 0.5772 0.3846 65 E 0.0499 0.6605 0.2896 66 I 0.0528 0.6950 0.2522 67 Y 0.1027 0.5314 0.3658 68 R 0.0691 0.4246 0.5063 69 G 0.0974 0.1768 0.7257 70 A 0.1772 0.0961 0.7266 71 A 0.2743 0.1012 0.6245 72 L 0.8398 0.0528 0.1074 73 I 0.8650 0.0432 0.0918 74 Y 0.8493 0.0459 0.1048 75 S 0.7147 0.0580 0.2274 76 I 0.3027 0.0544 0.6429 77 R 0.1108 0.0276 0.8616 78 P 0.0858 0.0286 0.8856 79 P 0.0667 0.2725 0.6607 80 A 0.0091 0.7171 0.2739 81 E 0.0110 0.7577 0.2313 82 I 0.0152 0.6661 0.3187 83 H 0.0183 0.6851 0.2966 84 S 0.0093 0.8250 0.1657 85 S 0.0087 0.9011 0.0902 86 L 0.0050 0.9368 0.0581 87 M 0.0049 0.9465 0.0486 88 R 0.0049 0.9460 0.0490 89 V 0.0050 0.9408 0.0542 90 A 0.0060 0.9296 0.0644 91 D 0.0056 0.8504 0.1441 92 A 0.0096 0.7177 0.2726 93 V 0.0674 0.3456 0.5870 94 G 0.0639 0.0217 0.9143 95 A 0.1070 0.0088 0.8841 96 R 0.2379 0.0207 0.7414 97 L 0.9009 0.0039 0.0952 98 I 0.9230 0.0036 0.0733 99 I 0.9192 0.0036 0.0772 100 K 0.8290 0.0092 0.1618 101 P 0.4393 0.0150 0.5457 102 L 0.1064 0.0615 0.8321 103 T 0.0854 0.0855 0.8291 104 G 0.0871 0.0812 0.8317 105 E 0.1682 0.0849 0.7468 106 D 0.2808 0.0762 0.6431 107 I 0.2593 0.1115 0.6292 108 V 0.2327 0.1441 0.6232 109 T 0.2094 0.1635 0.6271 110 E 0.2155 0.1278 0.6566 111 R 0.3574 0.0550 0.5876 112 K 0.5393 0.0312 0.4295 113 M 0.6537 0.0289 0.3174 114 K 0.6636 0.0418 0.2946 115 L 0.6080 0.0268 0.3651 116 V 0.3919 0.0309 0.5773 117 N 0.1859 0.0475 0.7666 118 Y 0.2443 0.0362 0.7195 119 G 0.4422 0.0322 0.5256 120 R 0.7191 0.0228 0.2581 121 T 0.8343 0.0197 0.1460 122 Y 0.8879 0.0115 0.1006 123 F 0.8938 0.0128 0.0934 124 Y 0.8815 0.0170 0.1015 125 E 0.8278 0.0317 0.1404 126 Y 0.7679 0.0436 0.1885 127 I 0.6248 0.0791 0.2961 128 A 0.4840 0.0940 0.4219 129 E 0.4150 0.0762 0.5088 130 V 0.3374 0.0953 0.5673 131 R 0.1992 0.0969 0.7039 132 S 0.1214 0.0739 0.8047 133 R 0.0378 0.0420 0.9202