# This file is the result of combining several RDB files, specifically # T0235.t04.dssp-ebghstl.rdb (weight 1.53986) # T0235.t04.stride-ebghtl.rdb (weight 1.24869) # T0235.t04.str2.rdb (weight 1.54758) # T0235.t04.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 T0235.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0235 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0235.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3.28994 # # ============================================ # Comments from T0235.t04.stride-ebghtl.rdb # ============================================ # TARGET T0235 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0235.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3.28994 # # ============================================ # Comments from T0235.t04.str2.rdb # ============================================ # TARGET T0235 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0235.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3.28994 # # ============================================ # Comments from T0235.t04.alpha.rdb # ============================================ # TARGET T0235 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0235.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3.28994 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0493 0.2130 0.7378 2 E 0.0596 0.5396 0.4008 3 Y 0.0802 0.6053 0.3144 4 A 0.0776 0.6331 0.2893 5 A 0.0853 0.6420 0.2727 6 E 0.1613 0.5330 0.3057 7 K 0.3003 0.4912 0.2085 8 V 0.3926 0.3839 0.2235 9 K 0.4508 0.3522 0.1970 10 V 0.3275 0.5103 0.1622 11 R 0.1642 0.6395 0.1962 12 D 0.0885 0.7378 0.1737 13 E 0.0505 0.7889 0.1606 14 L 0.0573 0.7733 0.1694 15 R 0.0709 0.7121 0.2170 16 K 0.0953 0.6921 0.2126 17 V 0.0992 0.6740 0.2268 18 E 0.0953 0.6076 0.2970 19 K 0.0575 0.6802 0.2624 20 E 0.0436 0.6650 0.2914 21 K 0.0371 0.6059 0.3570 22 N 0.0345 0.4545 0.5111 23 E 0.0283 0.5793 0.3923 24 K 0.0244 0.7207 0.2549 25 E 0.0294 0.8017 0.1689 26 R 0.0468 0.8065 0.1467 27 E 0.0831 0.7625 0.1543 28 I 0.0952 0.7114 0.1934 29 K 0.0903 0.6294 0.2802 30 R 0.0824 0.5719 0.3456 31 R 0.0930 0.4597 0.4473 32 K 0.1270 0.2760 0.5970 33 F 0.1279 0.0754 0.7966 34 D 0.0970 0.0209 0.8821 35 P 0.0541 0.1334 0.8125 36 S 0.0596 0.1224 0.8179 37 S 0.0589 0.1640 0.7771 38 S 0.0595 0.2516 0.6889 39 E 0.0758 0.2721 0.6520 40 N 0.1128 0.1909 0.6964 41 V 0.1753 0.0810 0.7437 42 M 0.1886 0.0581 0.7533 43 T 0.0957 0.0301 0.8741 44 P 0.0429 0.5897 0.3674 45 R 0.0138 0.8645 0.1217 46 E 0.0162 0.8965 0.0873 47 Q 0.0198 0.8999 0.0804 48 Y 0.0218 0.9043 0.0739 49 E 0.0197 0.9152 0.0651 50 T 0.0180 0.9175 0.0645 51 Q 0.0239 0.9070 0.0691 52 V 0.0358 0.8877 0.0765 53 A 0.0272 0.8646 0.1082 54 L 0.0298 0.7674 0.2028 55 N 0.0311 0.5885 0.3804 56 E 0.0371 0.4551 0.5078 57 S 0.0460 0.4399 0.5141 58 E 0.0135 0.7638 0.2227 59 K 0.0081 0.9069 0.0849 60 D 0.0092 0.9247 0.0661 61 Q 0.0063 0.9398 0.0539 62 W 0.0054 0.9424 0.0521 63 L 0.0048 0.9542 0.0410 64 E 0.0047 0.9560 0.0393 65 E 0.0048 0.9555 0.0397 66 Y 0.0052 0.9422 0.0526 67 K 0.0061 0.9203 0.0736 68 K 0.0095 0.8331 0.1573 69 H 0.0167 0.6414 0.3419 70 F 0.0641 0.0606 0.8754 71 P 0.0470 0.0686 0.8844 72 P 0.0210 0.2970 0.6820 73 N 0.0555 0.2992 0.6453 74 L 0.0441 0.4534 0.5024 75 E 0.0429 0.3212 0.6359 76 K 0.0540 0.1871 0.7589 77 G 0.0444 0.0807 0.8749 78 E 0.1046 0.0610 0.8344 79 N 0.1149 0.0171 0.8680 80 P 0.0392 0.0706 0.8902