# This file is the result of combining several RDB files, specifically # T0359.t04.dssp-ebghstl.rdb (weight 1.53986) # T0359.t04.stride-ebghtl.rdb (weight 1.24869) # T0359.t04.str2.rdb (weight 1.54758) # T0359.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 T0359.t04.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.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 1676 # # ============================================ # Comments from T0359.t04.stride-ebghtl.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t04.str2.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ # Comments from T0359.t04.alpha.rdb # ============================================ # TARGET T0359 # 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 T0359.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 1676 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0751 0.0248 0.9001 2 M 0.0941 0.0656 0.8403 3 S 0.1059 0.1035 0.7906 4 E 0.2328 0.0647 0.7024 5 T 0.5541 0.0103 0.4356 6 F 0.8273 0.0056 0.1671 7 D 0.9039 0.0033 0.0928 8 V 0.9034 0.0036 0.0930 9 E 0.9251 0.0034 0.0715 10 L 0.8996 0.0038 0.0966 11 T 0.8018 0.0047 0.1935 12 K 0.5845 0.0312 0.3843 13 N 0.3014 0.0243 0.6743 14 V 0.1192 0.0715 0.8094 15 Q 0.0906 0.0799 0.8295 16 G 0.1927 0.0667 0.7406 17 L 0.3860 0.0290 0.5850 18 G 0.7453 0.0111 0.2436 19 I 0.8886 0.0040 0.1074 20 T 0.9155 0.0038 0.0808 21 I 0.8999 0.0042 0.0960 22 A 0.7823 0.0217 0.1960 23 G 0.5560 0.0224 0.4216 24 Y 0.4450 0.0247 0.5303 25 I 0.4015 0.0475 0.5511 26 G 0.2150 0.0384 0.7465 27 D 0.1026 0.1147 0.7827 28 K 0.0591 0.2806 0.6603 29 K 0.0781 0.2726 0.6493 30 L 0.1268 0.1802 0.6929 31 E 0.1473 0.0609 0.7918 32 P 0.1180 0.0990 0.7830 33 S 0.1616 0.0644 0.7740 34 G 0.5121 0.0321 0.4557 35 I 0.8293 0.0064 0.1642 36 F 0.9051 0.0049 0.0900 37 V 0.9060 0.0045 0.0895 38 K 0.8250 0.0295 0.1455 39 S 0.7792 0.0094 0.2114 40 I 0.7234 0.0101 0.2665 41 T 0.3976 0.0231 0.5793 42 K 0.0905 0.0921 0.8175 43 S 0.0419 0.0693 0.8888 44 S 0.1120 0.0745 0.8135 45 A 0.1014 0.4608 0.4378 46 V 0.1313 0.4909 0.3779 47 E 0.1396 0.4841 0.3764 48 H 0.1617 0.3732 0.4651 49 D 0.1176 0.1124 0.7700 50 G 0.0946 0.0537 0.8517 51 R 0.3031 0.0340 0.6628 52 I 0.5290 0.0122 0.4588 53 Q 0.2024 0.0199 0.7777 54 I 0.0683 0.0930 0.8387 55 G 0.0745 0.0377 0.8878 56 D 0.3553 0.0189 0.6258 57 Q 0.8303 0.0059 0.1638 58 I 0.9175 0.0039 0.0785 59 I 0.9174 0.0042 0.0784 60 A 0.9105 0.0034 0.0861 61 V 0.8240 0.0126 0.1634 62 D 0.3053 0.0217 0.6730 63 G 0.1432 0.0353 0.8215 64 T 0.5558 0.0166 0.4276 65 N 0.6636 0.0144 0.3221 66 L 0.3075 0.0932 0.5994 67 Q 0.1123 0.1132 0.7745 68 G 0.0567 0.0767 0.8666 69 F 0.1507 0.0276 0.8217 70 T 0.1321 0.0395 0.8285 71 N 0.0068 0.9214 0.0717 72 Q 0.0047 0.9589 0.0364 73 Q 0.0047 0.9604 0.0349 74 A 0.0047 0.9610 0.0343 75 V 0.0046 0.9612 0.0341 76 E 0.0046 0.9610 0.0343 77 V 0.0047 0.9590 0.0364 78 L 0.0048 0.9509 0.0443 79 R 0.0051 0.9136 0.0814 80 H 0.0089 0.6976 0.2935 81 T 0.0583 0.2229 0.7188 82 G 0.0319 0.0400 0.9282 83 Q 0.0886 0.0183 0.8932 84 T 0.5736 0.0095 0.4169 85 V 0.8789 0.0039 0.1173 86 L 0.9207 0.0032 0.0761 87 L 0.9281 0.0033 0.0686 88 T 0.9232 0.0036 0.0732 89 L 0.9193 0.0035 0.0772 90 M 0.8293 0.0071 0.1637 91 R 0.6231 0.0097 0.3672 92 R 0.1751 0.0468 0.7781 93 G 0.0679 0.0319 0.9003 94 E 0.0849 0.0323 0.8828 95 T 0.0903 0.0346 0.8751 96 S 0.0953 0.0293 0.8754 97 V 0.0630 0.0366 0.9004