# This file is the result of combining several RDB files, specifically # TR453.t06.str2.rdb (weight 1.54425) # TR453.t06.str4.rdb (weight 0.924988) # TR453.t06.pb.rdb (weight 0.789901) # TR453.t06.bys.rdb (weight 0.748322) # TR453.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 TR453.t06.str2.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.str4.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.pb.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.bys.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.alpha.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.2382 0.1099 0.6520 2 E 0.3977 0.0765 0.5258 3 I 0.6269 0.0351 0.3380 4 V 0.6928 0.0259 0.2813 5 Q 0.7020 0.0177 0.2803 6 R 0.5345 0.0506 0.4149 7 E 0.3367 0.1642 0.4991 8 D 0.1139 0.1343 0.7518 9 G 0.0965 0.0736 0.8299 10 S 0.5168 0.0179 0.4653 11 W 0.7313 0.0099 0.2588 12 L 0.7740 0.0118 0.2142 13 V 0.7782 0.0114 0.2104 14 D 0.6468 0.0364 0.3167 15 G 0.5733 0.0741 0.3527 16 M 0.5097 0.0832 0.4071 17 V 0.5322 0.0367 0.4311 18 S 0.2582 0.0311 0.7107 19 L 0.0284 0.6947 0.2768 20 D 0.0117 0.8314 0.1569 21 R 0.0113 0.8854 0.1032 22 F 0.0129 0.8846 0.1026 23 R 0.0098 0.8995 0.0908 24 E 0.0103 0.8935 0.0962 25 F 0.0227 0.7771 0.2001 26 F 0.0779 0.4813 0.4408 27 E 0.0876 0.3256 0.5869 28 L 0.2119 0.1813 0.6068 29 E 0.2366 0.1056 0.6579 30 A 0.2844 0.0549 0.6608 31 P 0.2322 0.0681 0.6996 32 L 0.2370 0.0440 0.7191 33 P 0.1437 0.1772 0.6791 34 G 0.1007 0.2102 0.6891 35 E 0.1686 0.1936 0.6379 36 A 0.1256 0.2308 0.6436 37 G 0.1000 0.1228 0.7772 38 G 0.1259 0.1141 0.7600 39 N 0.2382 0.1255 0.6363 40 I 0.3376 0.2106 0.4518 41 H 0.3363 0.2986 0.3651 42 T 0.3476 0.3420 0.3105 43 L 0.1231 0.6776 0.1993 44 A 0.0631 0.7974 0.1395 45 G 0.0492 0.8474 0.1034 46 V 0.0239 0.8983 0.0779 47 M 0.0245 0.8977 0.0777 48 L 0.0144 0.9011 0.0845 49 Y 0.0136 0.8809 0.1056 50 Q 0.0239 0.7764 0.1997 51 L 0.0589 0.3303 0.6109 52 G 0.0435 0.1246 0.8320 53 R 0.1679 0.0776 0.7545 54 V 0.2522 0.0311 0.7167 55 P 0.2392 0.0474 0.7135 56 S 0.2314 0.0650 0.7036 57 V 0.2255 0.2173 0.5572 58 T 0.2241 0.1260 0.6499 59 D 0.5025 0.0503 0.4472 60 R 0.7241 0.0111 0.2648 61 F 0.7652 0.0105 0.2243 62 E 0.7415 0.0100 0.2484 63 W 0.6506 0.0317 0.3177 64 N 0.3216 0.0728 0.6056 65 G 0.1895 0.0587 0.7518 66 F 0.5989 0.0131 0.3880 67 S 0.7287 0.0119 0.2594 68 F 0.7957 0.0052 0.1991 69 E 0.7912 0.0070 0.2018 70 V 0.7360 0.0070 0.2570 71 V 0.7191 0.0178 0.2631 72 D 0.7041 0.0202 0.2757 73 M 0.5627 0.0759 0.3614 74 D 0.3224 0.1025 0.5751 75 R 0.1920 0.1745 0.6336 76 T 0.3077 0.1455 0.5468 77 R 0.5064 0.0757 0.4179 78 V 0.6128 0.0263 0.3609 79 D 0.5666 0.0617 0.3717 80 K 0.7831 0.0110 0.2059 81 I 0.7669 0.0068 0.2264 82 L 0.7705 0.0076 0.2219 83 V 0.7559 0.0075 0.2366 84 Q 0.6838 0.0144 0.3018 85 R 0.4991 0.0365 0.4644 86 H 0.2812 0.0643 0.6545 87 H 0.2131 0.1063 0.6807