# This file is the result of combining several RDB files, specifically # T0359.t06.dssp-ebghstl.rdb (weight 1.53986) # T0359.t06.stride-ebghtl.rdb (weight 1.24869) # T0359.t06.str2.rdb (weight 1.54758) # T0359.t06.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 T0359.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.stride-ebghtl.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.str2.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ # Comments from T0359.t06.alpha.rdb # ============================================ # TARGET T0359 # Using neural net t06-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 T0359.t06-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 1947 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0657 0.0182 0.9161 2 M 0.0862 0.0493 0.8645 3 S 0.1006 0.0632 0.8362 4 E 0.2234 0.0400 0.7366 5 T 0.5939 0.0073 0.3988 6 F 0.8293 0.0049 0.1658 7 D 0.9077 0.0031 0.0891 8 V 0.9086 0.0035 0.0879 9 E 0.9188 0.0035 0.0777 10 L 0.8959 0.0035 0.1006 11 T 0.7736 0.0049 0.2215 12 K 0.5497 0.0226 0.4278 13 N 0.2547 0.0243 0.7210 14 V 0.1129 0.0882 0.7990 15 Q 0.0897 0.0863 0.8241 16 G 0.1937 0.0626 0.7437 17 L 0.4062 0.0293 0.5645 18 G 0.7495 0.0115 0.2389 19 I 0.8823 0.0039 0.1138 20 T 0.9066 0.0042 0.0892 21 I 0.9007 0.0048 0.0945 22 A 0.8007 0.0208 0.1785 23 G 0.5778 0.0182 0.4041 24 Y 0.3884 0.0283 0.5833 25 I 0.3259 0.0656 0.6085 26 G 0.1798 0.0568 0.7633 27 D 0.1226 0.1008 0.7766 28 K 0.0977 0.2095 0.6929 29 K 0.1225 0.1879 0.6895 30 L 0.1628 0.1377 0.6995 31 E 0.1367 0.0568 0.8065 32 P 0.1191 0.0881 0.7928 33 S 0.1598 0.0711 0.7690 34 G 0.5412 0.0252 0.4336 35 I 0.8335 0.0050 0.1615 36 F 0.9025 0.0048 0.0927 37 V 0.8947 0.0058 0.0994 38 K 0.8283 0.0309 0.1408 39 S 0.8178 0.0083 0.1739 40 I 0.7163 0.0109 0.2728 41 T 0.4069 0.0210 0.5721 42 K 0.1008 0.1167 0.7825 43 S 0.0591 0.0849 0.8559 44 S 0.1370 0.1063 0.7567 45 A 0.0989 0.4804 0.4207 46 V 0.1101 0.5316 0.3583 47 E 0.1158 0.5115 0.3727 48 H 0.1306 0.4301 0.4393 49 D 0.0944 0.1549 0.7506 50 G 0.0562 0.0701 0.8737 51 R 0.2419 0.0455 0.7126 52 I 0.4788 0.0172 0.5040 53 Q 0.1551 0.0192 0.8257 54 I 0.0453 0.1110 0.8436 55 G 0.0511 0.0461 0.9028 56 D 0.3511 0.0258 0.6231 57 Q 0.8005 0.0122 0.1873 58 I 0.9049 0.0093 0.0858 59 I 0.8710 0.0146 0.1144 60 A 0.9087 0.0057 0.0856 61 V 0.8256 0.0156 0.1588 62 D 0.2838 0.0266 0.6896 63 G 0.1092 0.0365 0.8542 64 T 0.6468 0.0159 0.3372 65 N 0.6835 0.0135 0.3030 66 L 0.2926 0.1647 0.5427 67 Q 0.0998 0.1597 0.7404 68 G 0.0593 0.0951 0.8456 69 F 0.1624 0.0238 0.8138 70 T 0.1359 0.0303 0.8338 71 N 0.0063 0.9103 0.0834 72 Q 0.0047 0.9566 0.0387 73 Q 0.0047 0.9589 0.0364 74 A 0.0047 0.9613 0.0341 75 V 0.0047 0.9611 0.0343 76 E 0.0046 0.9607 0.0346 77 V 0.0047 0.9582 0.0371 78 L 0.0048 0.9518 0.0434 79 R 0.0052 0.9129 0.0818 80 H 0.0087 0.7106 0.2807 81 T 0.0583 0.1981 0.7435 82 G 0.0285 0.0435 0.9280 83 Q 0.0867 0.0227 0.8907 84 T 0.5253 0.0096 0.4651 85 V 0.8652 0.0039 0.1309 86 L 0.9216 0.0033 0.0751 87 L 0.9291 0.0033 0.0676 88 T 0.9239 0.0037 0.0724 89 L 0.9172 0.0036 0.0792 90 M 0.8145 0.0070 0.1785 91 R 0.5563 0.0100 0.4337 92 R 0.1531 0.0512 0.7957 93 G 0.0932 0.0542 0.8526 94 E 0.1108 0.0770 0.8121 95 T 0.1437 0.0612 0.7951 96 S 0.1166 0.0338 0.8496 97 V 0.0495 0.0298 0.9207