# This file is the result of combining several RDB files, specifically # TR429.t06.str2.rdb (weight 1.54425) # TR429.t06.str4.rdb (weight 0.924988) # TR429.t06.pb.rdb (weight 0.789901) # TR429.t06.bys.rdb (weight 0.748322) # TR429.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 TR429.t06.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.26435 # # ============================================ # Comments from TR429.t06.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.26435 # # ============================================ # Comments from TR429.t06.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.26435 # # ============================================ # Comments from TR429.t06.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.26435 # # ============================================ # Comments from TR429.t06.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.26435 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2106 0.0861 0.7033 2 T 0.1607 0.2200 0.6194 3 E 0.1824 0.1998 0.6177 4 L 0.3072 0.1395 0.5533 5 G 0.3804 0.0963 0.5233 6 L 0.5555 0.0917 0.3528 7 Y 0.5908 0.0819 0.3273 8 K 0.5260 0.0985 0.3755 9 V 0.3652 0.1793 0.4555 10 N 0.2934 0.2034 0.5032 11 E 0.3140 0.2508 0.4352 12 Y 0.4311 0.1673 0.4015 13 V 0.4929 0.0922 0.4149 14 D 0.3123 0.0928 0.5949 15 A 0.1158 0.4895 0.3946 16 R 0.0982 0.4807 0.4211 17 D 0.1518 0.4018 0.4464 18 T 0.1029 0.4110 0.4861 19 N 0.1405 0.3076 0.5519 20 M 0.1596 0.2554 0.5850 21 G 0.1998 0.1913 0.6089 22 A 0.5197 0.1555 0.3248 23 W 0.6552 0.1055 0.2393 24 F 0.6527 0.1468 0.2005 25 E 0.6692 0.1277 0.2031 26 A 0.7339 0.0706 0.1955 27 Q 0.7110 0.0826 0.2064 28 V 0.6884 0.0811 0.2305 29 V 0.6122 0.0956 0.2921 30 R 0.6111 0.0891 0.2998 31 V 0.5520 0.0904 0.3576 32 T 0.4921 0.0935 0.4144 33 R 0.3216 0.1611 0.5173 34 K 0.2601 0.1281 0.6119 35 A 0.2395 0.0540 0.7064 36 P 0.1723 0.1413 0.6863 37 S 0.1497 0.1701 0.6801 38 R 0.1367 0.2105 0.6529 39 D 0.1531 0.1355 0.7115 40 E 0.2385 0.0561 0.7054 41 P 0.2297 0.0974 0.6729 42 C 0.2272 0.1326 0.6403 43 S 0.1849 0.1756 0.6395 44 S 0.1511 0.2133 0.6357 45 T 0.1479 0.2152 0.6369 46 S 0.1699 0.1536 0.6765 47 R 0.2281 0.0855 0.6864 48 P 0.1972 0.1530 0.6498 49 A 0.2289 0.1650 0.6060 50 L 0.2050 0.1886 0.6065 51 E 0.1356 0.3513 0.5131 52 E 0.1617 0.3352 0.5031 53 D 0.3125 0.1817 0.5058 54 V 0.5925 0.0865 0.3210 55 I 0.6884 0.0478 0.2638 56 Y 0.7651 0.0251 0.2098 57 H 0.7700 0.0159 0.2141 58 V 0.7672 0.0132 0.2196 59 K 0.6840 0.0201 0.2959 60 Y 0.4991 0.0759 0.4250 61 D 0.2281 0.1931 0.5788 62 D 0.1807 0.1700 0.6493 63 Y 0.2715 0.0633 0.6651 64 P 0.1394 0.2569 0.6037 65 E 0.0641 0.3614 0.5745 66 N 0.0831 0.1760 0.7409 67 G 0.1589 0.0905 0.7506 68 V 0.5097 0.0302 0.4601 69 V 0.6756 0.0281 0.2963 70 Q 0.7004 0.0242 0.2754 71 M 0.6374 0.0279 0.3347 72 N 0.4121 0.0400 0.5478 73 S 0.2388 0.2046 0.5566 74 R 0.1598 0.3289 0.5113 75 D 0.1937 0.2381 0.5682 76 V 0.3087 0.1226 0.5688 77 R 0.3300 0.0852 0.5848 78 A 0.2661 0.2389 0.4950 79 R 0.1922 0.2921 0.5158 80 A 0.2241 0.2192 0.5567