# This file is the result of combining several RDB files, specifically # T0363.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0363.t2k.stride-ebghtl.rdb (weight 1.24869) # T0363.t2k.str2.rdb (weight 1.54758) # T0363.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 T0363.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0363 # 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 T0363.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 105 # # ============================================ # Comments from T0363.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0363 # 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 T0363.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 105 # # ============================================ # Comments from T0363.t2k.str2.rdb # ============================================ # TARGET T0363 # 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 T0363.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 105 # # ============================================ # Comments from T0363.t2k.alpha.rdb # ============================================ # TARGET T0363 # 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 T0363.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 105 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2307 0.0976 0.6717 2 A 0.2705 0.0791 0.6504 3 H 0.2526 0.0807 0.6668 4 H 0.1777 0.1047 0.7176 5 H 0.1071 0.2416 0.6514 6 H 0.0967 0.2182 0.6851 7 H 0.1270 0.1551 0.7179 8 H 0.0742 0.1772 0.7486 9 S 0.0908 0.1300 0.7793 10 L 0.0558 0.1797 0.7645 11 N 0.0701 0.1423 0.7876 12 Q 0.3178 0.0523 0.6299 13 I 0.6394 0.0071 0.3534 14 N 0.8866 0.0040 0.1094 15 I 0.9211 0.0035 0.0754 16 E 0.9243 0.0036 0.0721 17 I 0.9301 0.0030 0.0669 18 A 0.8973 0.0101 0.0927 19 Y 0.8959 0.0043 0.0998 20 A 0.7407 0.0087 0.2506 21 F 0.3234 0.0114 0.6652 22 P 0.0908 0.1296 0.7796 23 E 0.0880 0.1423 0.7697 24 R 0.4035 0.1021 0.4944 25 Y 0.6590 0.0122 0.3288 26 Y 0.8600 0.0074 0.1326 27 L 0.9202 0.0031 0.0767 28 K 0.8981 0.0063 0.0956 29 S 0.9209 0.0031 0.0760 30 F 0.8797 0.0042 0.1160 31 Q 0.8464 0.0042 0.1495 32 V 0.5857 0.0082 0.4061 33 D 0.1524 0.0216 0.8260 34 E 0.0276 0.0724 0.9000 35 G 0.0300 0.0453 0.9247 36 I 0.1960 0.0226 0.7813 37 T 0.3163 0.0529 0.6307 38 V 0.0067 0.9364 0.0569 39 Q 0.0050 0.9526 0.0424 40 T 0.0049 0.9552 0.0398 41 A 0.0047 0.9564 0.0389 42 I 0.0048 0.9550 0.0402 43 T 0.0051 0.9305 0.0645 44 Q 0.0057 0.8307 0.1636 45 S 0.0461 0.4702 0.4837 46 G 0.0401 0.1946 0.7653 47 I 0.0258 0.4070 0.5672 48 L 0.0335 0.5903 0.3761 49 S 0.0330 0.5820 0.3850 50 Q 0.0462 0.5145 0.4393 51 F 0.1077 0.1823 0.7100 52 P 0.0496 0.1563 0.7940 53 E 0.0883 0.1410 0.7708 54 I 0.2538 0.0730 0.6732 55 D 0.2112 0.0477 0.7410 56 L 0.0249 0.5979 0.3772 57 S 0.0159 0.5476 0.4365 58 T 0.0484 0.4410 0.5106 59 N 0.1341 0.0905 0.7755 60 K 0.2342 0.0586 0.7072 61 I 0.7669 0.0244 0.2087 62 G 0.8003 0.0273 0.1724 63 I 0.8137 0.0356 0.1507 64 F 0.6178 0.0489 0.3332 65 S 0.4339 0.0450 0.5211 66 R 0.4461 0.0424 0.5115 67 P 0.5930 0.0312 0.3759 68 I 0.4508 0.0243 0.5248 69 K 0.2748 0.0266 0.6985 70 L 0.1044 0.2214 0.6742 71 T 0.0705 0.2827 0.6468 72 D 0.1457 0.1907 0.6637 73 V 0.2701 0.1079 0.6220 74 L 0.2642 0.0490 0.6867 75 K 0.1095 0.0448 0.8458 76 E 0.0266 0.1193 0.8542 77 G 0.0337 0.0517 0.9146 78 D 0.1612 0.0376 0.8011 79 R 0.5960 0.0163 0.3877 80 I 0.8062 0.0131 0.1807 81 E 0.8872 0.0069 0.1059 82 I 0.8771 0.0087 0.1142 83 Y 0.7846 0.0102 0.2051 84 R 0.5353 0.0271 0.4375 85 P 0.3686 0.0591 0.5723 86 L 0.3770 0.1066 0.5163 87 L 0.4400 0.0654 0.4946 88 A 0.3962 0.0302 0.5736 89 D 0.2330 0.0212 0.7458 90 P 0.0136 0.6805 0.3059 91 K 0.0099 0.8161 0.1739 92 E 0.0137 0.8559 0.1305 93 I 0.0242 0.8198 0.1560 94 R 0.0470 0.7714 0.1816 95 R 0.0461 0.6788 0.2751 96 E 0.0617 0.3860 0.5522 97 G 0.0408 0.0483 0.9109