# This file is the result of combining several RDB files, specifically # T0377.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0377.t2k.stride-ebghtl.rdb (weight 1.24869) # T0377.t2k.str2.rdb (weight 1.54758) # T0377.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 T0377.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0377 # 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 T0377.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 58 # # ============================================ # Comments from T0377.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0377 # 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 T0377.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 58 # # ============================================ # Comments from T0377.t2k.str2.rdb # ============================================ # TARGET T0377 # 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 T0377.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 58 # # ============================================ # Comments from T0377.t2k.alpha.rdb # ============================================ # TARGET T0377 # 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 T0377.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 58 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1834 0.0362 0.7805 2 A 0.4426 0.0248 0.5326 3 M 0.7893 0.0078 0.2029 4 L 0.8878 0.0057 0.1065 5 Y 0.9261 0.0041 0.0698 6 L 0.9262 0.0049 0.0688 7 I 0.9245 0.0061 0.0695 8 F 0.9007 0.0212 0.0781 9 Y 0.8467 0.0182 0.1351 10 D 0.5905 0.0218 0.3877 11 I 0.1863 0.1246 0.6891 12 T 0.0569 0.1775 0.7656 13 D 0.0291 0.2368 0.7341 14 D 0.0160 0.3822 0.6018 15 N 0.0155 0.6461 0.3385 16 L 0.0219 0.7806 0.1975 17 R 0.0078 0.8983 0.0939 18 N 0.0060 0.9378 0.0562 19 R 0.0049 0.9527 0.0424 20 V 0.0047 0.9584 0.0368 21 A 0.0047 0.9603 0.0350 22 E 0.0047 0.9596 0.0357 23 F 0.0047 0.9575 0.0378 24 L 0.0049 0.9513 0.0438 25 K 0.0051 0.9336 0.0613 26 K 0.0063 0.8642 0.1295 27 K 0.0395 0.4832 0.4773 28 G 0.0400 0.1853 0.7746 29 L 0.0889 0.1178 0.7932 30 D 0.2681 0.1686 0.5633 31 R 0.4739 0.1882 0.3379 32 I 0.5867 0.1636 0.2497 33 Q 0.6462 0.1542 0.1996 34 Y 0.6239 0.1225 0.2537 35 S 0.6023 0.1419 0.2558 36 V 0.6168 0.1595 0.2237 37 F 0.6239 0.1669 0.2092 38 M 0.5601 0.1467 0.2932 39 G 0.4758 0.1047 0.4196 40 D 0.4778 0.0544 0.4678 41 L 0.2520 0.0344 0.7136 42 N 0.0931 0.0243 0.8825 43 S 0.0067 0.8916 0.1017 44 S 0.0051 0.9322 0.0627 45 R 0.0054 0.9401 0.0545 46 L 0.0047 0.9560 0.0393 47 K 0.0048 0.9544 0.0408 48 D 0.0048 0.9539 0.0413 49 V 0.0048 0.9546 0.0406 50 E 0.0052 0.9541 0.0408 51 A 0.0056 0.9471 0.0473 52 G 0.0060 0.9309 0.0630 53 L 0.0127 0.9185 0.0687 54 K 0.0134 0.8954 0.0912 55 I 0.0149 0.8779 0.1071 56 I 0.0234 0.8210 0.1556 57 G 0.0212 0.6834 0.2953 58 N 0.0336 0.4419 0.5244 59 R 0.0499 0.4202 0.5299 60 K 0.0636 0.3956 0.5408 61 K 0.0709 0.3039 0.6252 62 L 0.1631 0.2787 0.5581 63 Q 0.2211 0.1403 0.6387 64 E 0.1593 0.0920 0.7487 65 D 0.0562 0.2918 0.6520 66 E 0.0460 0.2954 0.6585 67 R 0.0820 0.1653 0.7526 68 F 0.1231 0.0638 0.8131 69 F 0.6908 0.0111 0.2981 70 I 0.9040 0.0040 0.0920 71 L 0.9160 0.0038 0.0802 72 I 0.9131 0.0036 0.0833 73 V 0.8448 0.0052 0.1500 74 P 0.7069 0.0063 0.2869 75 I 0.3245 0.0160 0.6595 76 T 0.1506 0.0225 0.8269 77 E 0.0213 0.5656 0.4130 78 N 0.0231 0.6213 0.3556 79 Q 0.0426 0.6714 0.2859 80 F 0.1044 0.6076 0.2880 81 R 0.1867 0.5385 0.2749 82 E 0.2992 0.4548 0.2459 83 R 0.5012 0.2871 0.2118 84 I 0.5780 0.2382 0.1838 85 V 0.5788 0.2100 0.2112 86 I 0.3556 0.1627 0.4816 87 G 0.1723 0.0546 0.7731 88 Y 0.1029 0.0474 0.8497 89 S 0.1034 0.0640 0.8326 90 G 0.1082 0.1003 0.7915 91 S 0.0982 0.1181 0.7837 92 E 0.1343 0.1455 0.7203 93 R 0.1568 0.0889 0.7543 94 E 0.1140 0.0480 0.8380 95 E 0.0972 0.1276 0.7752 96 K 0.1021 0.1055 0.7924 97 S 0.2128 0.0776 0.7096 98 N 0.5798 0.0279 0.3924 99 V 0.7473 0.0137 0.2390 100 V 0.5871 0.0094 0.4035 101 W 0.0855 0.0092 0.9052