# This file is the result of combining several RDB files, specifically # T0397.t06.str2.rdb (weight 1.54425) # T0397.t06.str4.rdb (weight 0.924988) # T0397.t06.pb.rdb (weight 0.789901) # T0397.t06.bys.rdb (weight 0.748322) # T0397.t06.alpha.rdb (weight 0.678173) # 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 T0397.t06.str2.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-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 T0397.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 3.87914 # # ============================================ # Comments from T0397.t06.str4.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0397.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 3.87914 # # ============================================ # Comments from T0397.t06.pb.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0397.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 3.87914 # # ============================================ # Comments from T0397.t06.bys.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0397.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 3.87914 # # ============================================ # Comments from T0397.t06.alpha.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-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 T0397.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 3.87914 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.2165 0.0760 0.7075 2 T 0.3395 0.0748 0.5857 3 K 0.5989 0.0493 0.3518 4 L 0.6983 0.0275 0.2742 5 I 0.7509 0.0204 0.2287 6 S 0.7284 0.0140 0.2576 7 V 0.6927 0.0133 0.2940 8 P 0.5364 0.0145 0.4491 9 A 0.3356 0.1500 0.5144 10 E 0.2600 0.1436 0.5964 11 G 0.2355 0.1029 0.6615 12 Y 0.4298 0.0652 0.5050 13 K 0.6105 0.0465 0.3430 14 V 0.6283 0.0430 0.3287 15 Y 0.6306 0.0257 0.3437 16 P 0.5642 0.0609 0.3749 17 I 0.5734 0.1081 0.3185 18 M 0.5191 0.1329 0.3481 19 D 0.4033 0.1321 0.4646 20 F 0.2142 0.2444 0.5414 21 G 0.1978 0.2084 0.5938 22 F 0.4003 0.2133 0.3864 23 R 0.5165 0.2108 0.2727 24 V 0.5075 0.1954 0.2971 25 L 0.4109 0.1764 0.4127 26 K 0.1843 0.1506 0.6651 27 G 0.1057 0.1003 0.7940 28 Y 0.3424 0.0641 0.5935 29 R 0.5185 0.1021 0.3795 30 L 0.6042 0.1230 0.2728 31 A 0.6887 0.0840 0.2273 32 T 0.7399 0.0564 0.2036 33 L 0.7186 0.0517 0.2297 34 E 0.6846 0.0509 0.2645 35 S 0.5007 0.0514 0.4479 36 K 0.2326 0.2376 0.5298 37 K 0.2164 0.1174 0.6662 38 G 0.3193 0.0588 0.6219 39 D 0.5714 0.0318 0.3968 40 L 0.7211 0.0116 0.2673 41 R 0.7252 0.0278 0.2470 42 Y 0.7655 0.0114 0.2231 43 V 0.7066 0.0262 0.2672 44 N 0.5896 0.0313 0.3791 45 S 0.4305 0.0219 0.5477 46 P 0.2613 0.0679 0.6709 47 V 0.2312 0.1328 0.6360 48 S 0.2299 0.1006 0.6695 49 G 0.3929 0.0454 0.5616 50 T 0.7242 0.0111 0.2647 51 V 0.7961 0.0053 0.1986 52 I 0.8068 0.0066 0.1866 53 F 0.7791 0.0082 0.2127 54 M 0.6773 0.0384 0.2843 55 N 0.5300 0.0685 0.4016 56 E 0.4084 0.0785 0.5131 57 I 0.3101 0.0352 0.6547 58 P 0.2067 0.1010 0.6924 59 S 0.1483 0.2250 0.6267 60 E 0.1342 0.2229 0.6429 61 R 0.2313 0.1070 0.6617 62 A 0.2202 0.2123 0.5675 63 N 0.3367 0.1240 0.5393 64 Y 0.7137 0.0269 0.2595 65 V 0.7613 0.0163 0.2224 66 F 0.8127 0.0093 0.1780 67 Y 0.7933 0.0120 0.1947 68 M 0.7374 0.0169 0.2457 69 L 0.6095 0.0179 0.3726 70 E 0.3131 0.1083 0.5786 71 E 0.1854 0.1699 0.6447