# This file is the result of combining several RDB files, specifically # T0150.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0150.t2k.stride-ebghtl.rdb (weight 1.24869) # T0150.t2k.str.rdb (weight 1.53983) # T0150.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 T0150.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0150 # 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 T0150.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 77 # # ============================================ # Comments from T0150.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0150 # 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 T0150.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 77 # # ============================================ # Comments from T0150.t2k.str.rdb # ============================================ # TARGET T0150 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0150.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 77 # # ============================================ # Comments from T0150.t2k.alpha.rdb # ============================================ # TARGET T0150 # 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 T0150.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 77 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0249 0.2116 0.7635 2 S 0.0258 0.5665 0.4077 3 V 0.0115 0.7806 0.2079 4 D 0.0122 0.8120 0.1758 5 F 0.0047 0.9145 0.0808 6 A 0.0045 0.9445 0.0510 7 F 0.0045 0.9538 0.0417 8 E 0.0045 0.9551 0.0404 9 L 0.0045 0.9552 0.0402 10 R 0.0045 0.9550 0.0405 11 K 0.0046 0.9529 0.0424 12 A 0.0048 0.9510 0.0442 13 Q 0.0065 0.9332 0.0603 14 D 0.0071 0.8552 0.1377 15 T 0.0431 0.4184 0.5385 16 G 0.0306 0.0520 0.9174 17 K 0.1180 0.0446 0.8375 18 I 0.5272 0.0451 0.4277 19 V 0.5443 0.0735 0.3822 20 M 0.3066 0.1892 0.5042 21 G 0.1162 0.2737 0.6100 22 A 0.0415 0.7282 0.2304 23 R 0.0212 0.8956 0.0832 24 K 0.0150 0.9253 0.0597 25 S 0.0113 0.9437 0.0450 26 I 0.0078 0.9547 0.0375 27 Q 0.0062 0.9573 0.0365 28 Y 0.0049 0.9587 0.0364 29 A 0.0052 0.9512 0.0436 30 K 0.0051 0.9128 0.0821 31 M 0.0418 0.3730 0.5851 32 G 0.0224 0.0692 0.9083 33 G 0.0548 0.0435 0.9018 34 A 0.2432 0.0095 0.7473 35 K 0.5641 0.0172 0.4187 36 L 0.9209 0.0036 0.0755 37 I 0.9312 0.0036 0.0653 38 I 0.9285 0.0035 0.0679 39 V 0.8839 0.0060 0.1101 40 A 0.5723 0.0311 0.3966 41 R 0.1839 0.0832 0.7329 42 N 0.1089 0.0739 0.8172 43 A 0.0783 0.0439 0.8777 44 R 0.0575 0.0510 0.8915 45 P 0.0093 0.6387 0.3520 46 D 0.0102 0.6877 0.3021 47 I 0.0215 0.7893 0.1891 48 K 0.0253 0.8376 0.1371 49 E 0.0348 0.8218 0.1434 50 D 0.0285 0.8000 0.1715 51 I 0.0108 0.9114 0.0778 52 E 0.0057 0.9470 0.0474 53 Y 0.0056 0.9521 0.0423 54 Y 0.0049 0.9528 0.0423 55 A 0.0050 0.9493 0.0457 56 R 0.0055 0.9354 0.0591 57 L 0.0083 0.8559 0.1358 58 S 0.0488 0.3702 0.5810 59 G 0.0447 0.0242 0.9310 60 I 0.1035 0.0084 0.8881 61 P 0.3574 0.0073 0.6353 62 V 0.8595 0.0042 0.1363 63 Y 0.9116 0.0041 0.0844 64 E 0.9117 0.0040 0.0843 65 F 0.8738 0.0057 0.1205 66 E 0.5699 0.0204 0.4097 67 G 0.1584 0.0595 0.7822 68 T 0.1071 0.0586 0.8343 69 S 0.0324 0.7170 0.2507 70 V 0.0383 0.8235 0.1382 71 E 0.0603 0.8003 0.1393 72 L 0.0350 0.8550 0.1101 73 G 0.0350 0.8093 0.1557 74 T 0.0255 0.8147 0.1598 75 L 0.0289 0.7337 0.2374 76 L 0.0605 0.3885 0.5510 77 G 0.0462 0.0450 0.9088 78 R 0.1124 0.0303 0.8573 79 P 0.2020 0.0244 0.7736 80 H 0.3530 0.0163 0.6307 81 T 0.5632 0.0117 0.4250 82 V 0.8464 0.0056 0.1480 83 S 0.9101 0.0049 0.0850 84 A 0.9256 0.0035 0.0710 85 L 0.9193 0.0044 0.0763 86 A 0.9093 0.0041 0.0867 87 V 0.8742 0.0054 0.1204 88 V 0.7119 0.0112 0.2769 89 D 0.2881 0.0129 0.6990 90 P 0.0296 0.1686 0.8017 91 G 0.0297 0.1749 0.7954 92 E 0.0306 0.5903 0.3791 93 S 0.0194 0.7957 0.1849 94 R 0.0148 0.8469 0.1383 95 I 0.0186 0.8648 0.1166 96 L 0.0292 0.8418 0.1291 97 A 0.0381 0.7660 0.1959 98 L 0.0346 0.7006 0.2648 99 G 0.0582 0.4823 0.4594 100 G 0.0420 0.3757 0.5824 101 K 0.0366 0.2662 0.6972 102 E 0.0313 0.0625 0.9062