# This file is the result of combining several RDB files, specifically # T0386.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0386.t2k.stride-ebghtl.rdb (weight 1.24869) # T0386.t2k.str2.rdb (weight 1.54758) # T0386.t2k.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 T0386.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 5 # # ============================================ # Comments from T0386.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 5 # # ============================================ # Comments from T0386.t2k.str2.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 5 # # ============================================ # Comments from T0386.t2k.alpha.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0387 0.7246 0.2367 2 L 0.0146 0.8893 0.0961 3 K 0.0060 0.9376 0.0564 4 E 0.0054 0.9390 0.0556 5 F 0.0051 0.9375 0.0574 6 M 0.0048 0.9393 0.0558 7 H 0.0053 0.9229 0.0718 8 T 0.0067 0.8856 0.1077 9 M 0.0229 0.8378 0.1394 10 K 0.0214 0.7528 0.2258 11 N 0.0195 0.5955 0.3850 12 T 0.0498 0.3027 0.6475 13 G 0.0420 0.1003 0.8576 14 R 0.0780 0.0953 0.8267 15 N 0.1647 0.1072 0.7281 16 V 0.1783 0.1271 0.6946 17 N 0.1939 0.0862 0.7199 18 D 0.1807 0.1034 0.7159 19 R 0.4225 0.0432 0.5343 20 P 0.7451 0.0196 0.2352 21 V 0.8831 0.0120 0.1049 22 M 0.9090 0.0084 0.0826 23 V 0.9015 0.0093 0.0892 24 A 0.8153 0.0198 0.1649 25 K 0.6307 0.0342 0.3351 26 E 0.1246 0.0847 0.7907 27 G 0.0824 0.0475 0.8701 28 E 0.3848 0.0286 0.5867 29 T 0.6085 0.0233 0.3682 30 Y 0.5149 0.0438 0.4413 31 T 0.3441 0.0544 0.6014 32 G 0.3970 0.0450 0.5580 33 T 0.5977 0.0519 0.3505 34 Y 0.6819 0.0467 0.2714 35 R 0.4655 0.0781 0.4563 36 G 0.3031 0.0581 0.6388 37 A 0.2787 0.0809 0.6405 38 G 0.2770 0.1018 0.6212 39 L 0.2800 0.1453 0.5747 40 E 0.4423 0.0886 0.4691 41 G 0.6802 0.0422 0.2777 42 F 0.8518 0.0132 0.1350 43 A 0.9076 0.0071 0.0853 44 L 0.9078 0.0068 0.0854 45 N 0.9002 0.0041 0.0956 46 V 0.8232 0.0134 0.1634 47 K 0.3620 0.0473 0.5907 48 G 0.1940 0.0406 0.7654 49 A 0.6331 0.0139 0.3530 50 Y 0.8636 0.0059 0.1305 51 I 0.8826 0.0054 0.1119 52 I 0.7552 0.0282 0.2166 53 G 0.4081 0.0170 0.5749 54 N 0.1862 0.0398 0.7740 55 I 0.0563 0.3561 0.5876 56 D 0.0350 0.3724 0.5927 57 H 0.0592 0.2660 0.6747 58 L 0.1352 0.0507 0.8141 59 P 0.0842 0.0449 0.8710 60 P 0.0338 0.7206 0.2455 61 E 0.0338 0.7683 0.1980 62 Q 0.0582 0.7488 0.1931 63 L 0.1688 0.5495 0.2817 64 K 0.2199 0.4624 0.3177 65 I 0.2921 0.3265 0.3815 66 L 0.2133 0.1022 0.6845 67 K 0.0779 0.0412 0.8809 68 P 0.0271 0.0860 0.8869 69 G 0.0294 0.0507 0.9198 70 D 0.2206 0.0262 0.7531 71 K 0.6932 0.0219 0.2849 72 I 0.8403 0.0094 0.1503 73 T 0.8107 0.0107 0.1786 74 F 0.6037 0.0112 0.3850 75 T 0.0820 0.0187 0.8993