# This file is the result of combining several RDB files, specifically # T0309.t06.dssp-ebghstl.rdb (weight 1.53986) # T0309.t06.stride-ebghtl.rdb (weight 1.24869) # T0309.t06.str2.rdb (weight 1.54758) # T0309.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 T0309.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0629 0.2529 0.6842 2 A 0.0919 0.2555 0.6526 3 S 0.1072 0.2398 0.6530 4 K 0.1322 0.2544 0.6134 5 K 0.2684 0.2047 0.5269 6 V 0.4030 0.1704 0.4266 7 H 0.4882 0.1364 0.3754 8 Q 0.6723 0.1029 0.2248 9 I 0.6842 0.0932 0.2226 10 N 0.5885 0.0684 0.3432 11 V 0.5131 0.0918 0.3951 12 K 0.3233 0.1271 0.5496 13 G 0.3272 0.0853 0.5875 14 F 0.4593 0.0928 0.4479 15 F 0.5249 0.0680 0.4071 16 D 0.4526 0.0595 0.4879 17 M 0.3504 0.1022 0.5474 18 D 0.3785 0.1065 0.5150 19 V 0.5251 0.1679 0.3070 20 M 0.6270 0.1283 0.2447 21 E 0.6615 0.1287 0.2099 22 V 0.5858 0.1166 0.2976 23 T 0.4621 0.1153 0.4226 24 E 0.2790 0.2772 0.4438 25 Q 0.2203 0.2565 0.5232 26 T 0.2245 0.1616 0.6139 27 K 0.2198 0.2822 0.4980 28 E 0.3185 0.2580 0.4235 29 A 0.3567 0.2587 0.3846 30 E 0.3983 0.2645 0.3372 31 Y 0.4230 0.2106 0.3664 32 T 0.3835 0.2049 0.4115 33 Y 0.2778 0.2233 0.4989 34 D 0.2075 0.2089 0.5836 35 F 0.0138 0.8926 0.0937 36 K 0.0082 0.9329 0.0589 37 E 0.0117 0.9327 0.0556 38 I 0.0141 0.9238 0.0620 39 L 0.0148 0.9055 0.0796 40 S 0.0151 0.8486 0.1364 41 E 0.0179 0.7707 0.2114 42 F 0.0707 0.5067 0.4225 43 N 0.0604 0.1278 0.8119 44 G 0.0458 0.0597 0.8945 45 K 0.1508 0.0617 0.7875 46 N 0.3619 0.0260 0.6121 47 V 0.5516 0.0137 0.4347 48 S 0.7986 0.0074 0.1940 49 I 0.8638 0.0049 0.1312 50 T 0.8614 0.0062 0.1324 51 V 0.8127 0.0144 0.1729 52 K 0.6565 0.0305 0.3129 53 E 0.5893 0.0784 0.3323 54 E 0.3544 0.1520 0.4937 55 N 0.2789 0.1049 0.6162 56 E 0.3517 0.0559 0.5923 57 L 0.4308 0.0227 0.5465 58 P 0.3828 0.0292 0.5880 59 V 0.4557 0.0660 0.4783 60 K 0.3278 0.1165 0.5557 61 G 0.3370 0.1075 0.5555 62 V 0.5626 0.0935 0.3439 63 E 0.6876 0.0742 0.2382 64 M 0.5542 0.0804 0.3653 65 A 0.2357 0.0888 0.6755 66 G 0.0842 0.0540 0.8618 67 D 0.1089 0.0308 0.8603 68 P 0.0758 0.2414 0.6828 69 L 0.0772 0.3700 0.5528 70 E 0.0920 0.4325 0.4755 71 H 0.1129 0.4011 0.4860 72 H 0.1379 0.3260 0.5361 73 H 0.1303 0.2631 0.6066 74 H 0.1134 0.2000 0.6867 75 H 0.0932 0.1279 0.7789 76 H 0.0543 0.0398 0.9060