# This file is the result of combining several RDB files, specifically # T0275.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0275.t2k.stride-ebghtl.rdb (weight 1.24869) # T0275.t2k.str2.rdb (weight 1.54758) # T0275.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 T0275.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0275 # 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 T0275.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 806 # # ============================================ # Comments from T0275.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0275 # 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 T0275.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 806 # # ============================================ # Comments from T0275.t2k.str2.rdb # ============================================ # TARGET T0275 # 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 T0275.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 806 # # ============================================ # Comments from T0275.t2k.alpha.rdb # ============================================ # TARGET T0275 # 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 T0275.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 806 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0584 0.0369 0.9047 2 F 0.2192 0.0306 0.7502 3 K 0.3595 0.0566 0.5839 4 T 0.6256 0.0285 0.3459 5 I 0.8311 0.0119 0.1570 6 L 0.8827 0.0068 0.1106 7 L 0.8521 0.0081 0.1399 8 A 0.7176 0.0129 0.2695 9 Y 0.3993 0.0269 0.5737 10 D 0.1468 0.0289 0.8242 11 G 0.0456 0.0540 0.9004 12 S 0.0579 0.0490 0.8931 13 E 0.0114 0.8257 0.1630 14 H 0.0090 0.8672 0.1238 15 A 0.0063 0.9221 0.0716 16 R 0.0048 0.9530 0.0423 17 R 0.0048 0.9532 0.0420 18 A 0.0048 0.9533 0.0419 19 A 0.0047 0.9571 0.0383 20 E 0.0047 0.9578 0.0375 21 V 0.0047 0.9562 0.0391 22 A 0.0048 0.9543 0.0410 23 K 0.0048 0.9525 0.0427 24 A 0.0049 0.9443 0.0508 25 E 0.0049 0.9367 0.0584 26 A 0.0056 0.9275 0.0669 27 E 0.0069 0.8798 0.1133 28 A 0.0138 0.7555 0.2306 29 H 0.0455 0.2769 0.6776 30 G 0.0439 0.0179 0.9383 31 A 0.0860 0.0083 0.9057 32 R 0.5574 0.0047 0.4379 33 L 0.9171 0.0030 0.0799 34 I 0.9268 0.0039 0.0693 35 V 0.9338 0.0030 0.0632 36 V 0.9266 0.0035 0.0699 37 H 0.9114 0.0035 0.0851 38 A 0.8063 0.0052 0.1885 39 Y 0.6014 0.0104 0.3882 40 E 0.3519 0.0223 0.6258 41 P 0.1456 0.0753 0.7791 42 V 0.0855 0.1798 0.7346 43 P 0.0578 0.2754 0.6668 44 D 0.0571 0.2919 0.6510 45 Y 0.0556 0.2833 0.6611 46 L 0.0607 0.2817 0.6575 47 G 0.0531 0.2745 0.6724 48 E 0.0503 0.3442 0.6054 49 P 0.0505 0.3745 0.5750 50 F 0.0506 0.3980 0.5514 51 F 0.0293 0.6213 0.3495 52 E 0.0125 0.8024 0.1852 53 E 0.0106 0.8503 0.1391 54 A 0.0084 0.8690 0.1226 55 L 0.0067 0.8903 0.1029 56 R 0.0064 0.9022 0.0914 57 R 0.0063 0.9075 0.0862 58 R 0.0067 0.8970 0.0963 59 L 0.0060 0.9170 0.0770 60 E 0.0063 0.9220 0.0717 61 R 0.0058 0.9306 0.0637 62 A 0.0052 0.9338 0.0609 63 E 0.0050 0.9463 0.0487 64 G 0.0050 0.9460 0.0490 65 V 0.0048 0.9484 0.0468 66 L 0.0049 0.9450 0.0502 67 E 0.0049 0.9436 0.0515 68 E 0.0050 0.9352 0.0597 69 A 0.0054 0.9232 0.0714 70 R 0.0066 0.8949 0.0985 71 A 0.0087 0.8100 0.1813 72 L 0.0260 0.6401 0.3340 73 T 0.0446 0.2093 0.7462 74 G 0.0334 0.0365 0.9301 75 V 0.1194 0.0130 0.8676 76 P 0.4072 0.0121 0.5807 77 K 0.7340 0.0094 0.2566 78 E 0.7936 0.0119 0.1945 79 D 0.8063 0.0082 0.1855 80 A 0.8334 0.0092 0.1574 81 L 0.8539 0.0113 0.1347 82 L 0.7713 0.0248 0.2039 83 L 0.5885 0.0452 0.3664 84 E 0.1915 0.0632 0.7453 85 G 0.0631 0.0336 0.9033 86 V 0.0819 0.0444 0.8737 87 P 0.0197 0.7689 0.2114 88 A 0.0053 0.9294 0.0652 89 E 0.0051 0.9449 0.0500 90 A 0.0048 0.9517 0.0436 91 I 0.0047 0.9542 0.0411 92 L 0.0047 0.9533 0.0420 93 Q 0.0047 0.9513 0.0439 94 A 0.0047 0.9505 0.0448 95 A 0.0049 0.9414 0.0537 96 R 0.0051 0.9238 0.0710 97 A 0.0071 0.8303 0.1625 98 E 0.0418 0.4973 0.4609 99 K 0.0579 0.0421 0.9000 100 A 0.0997 0.0077 0.8927 101 D 0.1995 0.0403 0.7602 102 L 0.9270 0.0036 0.0695 103 I 0.9330 0.0032 0.0637 104 V 0.9294 0.0032 0.0674 105 M 0.8705 0.0124 0.1171 106 G 0.4091 0.0189 0.5720 107 T 0.1289 0.0631 0.8080 108 R 0.0934 0.0993 0.8073 109 G 0.0736 0.1144 0.8120 110 L 0.0582 0.1743 0.7675 111 G 0.0629 0.2531 0.6840 112 A 0.0618 0.4291 0.5091 113 L 0.1004 0.6050 0.2947 114 G 0.1133 0.6683 0.2184 115 S 0.1331 0.6497 0.2172 116 L 0.1719 0.5925 0.2356 117 F 0.2553 0.4549 0.2899 118 L 0.1759 0.3769 0.4472 119 G 0.0804 0.3533 0.5663 120 S 0.0561 0.6241 0.3198 121 Q 0.0121 0.9140 0.0738 122 S 0.0059 0.9413 0.0528 123 Q 0.0050 0.9488 0.0462 124 R 0.0050 0.9498 0.0452 125 V 0.0050 0.9443 0.0507 126 V 0.0061 0.9237 0.0702 127 A 0.0084 0.8271 0.1645 128 E 0.0211 0.5547 0.4242 129 A 0.0783 0.0685 0.8532 130 P 0.0367 0.0556 0.9076 131 C 0.0810 0.0126 0.9064 132 P 0.2248 0.0092 0.7660 133 V 0.8482 0.0051 0.1467 134 L 0.9201 0.0034 0.0766 135 L 0.9048 0.0035 0.0917 136 V 0.7208 0.0062 0.2730 137 R 0.0781 0.0122 0.9096