# This file is the result of combining several RDB files, specifically # T0474.t04.dssp-ebghstl.rdb (weight 1.53986) # T0474.t04.stride-ebghtl.rdb (weight 1.24869) # T0474.t04.str2.rdb (weight 1.54758) # T0474.t04.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 T0474.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0474 # Using neural net t04-2621-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 T0474.t04-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 16.4906 # # ============================================ # Comments from T0474.t04.stride-ebghtl.rdb # ============================================ # TARGET T0474 # Using neural net t04-2621-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 T0474.t04-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 16.4906 # # ============================================ # Comments from T0474.t04.str2.rdb # ============================================ # TARGET T0474 # Using neural net t04-2621-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 T0474.t04-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 16.4906 # # ============================================ # Comments from T0474.t04.alpha.rdb # ============================================ # TARGET T0474 # Using neural net t04-2621-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 T0474.t04-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 16.4906 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1157 0.1488 0.7355 2 N 0.1452 0.1838 0.6710 3 S 0.1449 0.4033 0.4518 4 L 0.1563 0.4365 0.4072 5 A 0.1756 0.4004 0.4240 6 G 0.2557 0.3208 0.4235 7 I 0.3956 0.3058 0.2986 8 D 0.4496 0.2174 0.3330 9 M 0.5448 0.1735 0.2817 10 G 0.6380 0.0909 0.2711 11 R 0.7792 0.0655 0.1553 12 I 0.8196 0.0490 0.1314 13 L 0.8444 0.0392 0.1164 14 L 0.7930 0.0318 0.1752 15 D 0.4795 0.0175 0.5030 16 L 0.0999 0.0593 0.8408 17 S 0.0546 0.0934 0.8520 18 N 0.0055 0.9377 0.0568 19 E 0.0048 0.9536 0.0416 20 V 0.0050 0.9507 0.0443 21 I 0.0048 0.9499 0.0453 22 K 0.0049 0.9042 0.0909 23 Q 0.0057 0.8320 0.1623 24 L 0.0064 0.8551 0.1386 25 D 0.0054 0.8993 0.0953 26 D 0.0061 0.9083 0.0856 27 L 0.0063 0.9166 0.0772 28 E 0.0082 0.8973 0.0946 29 V 0.0104 0.8768 0.1128 30 Q 0.0190 0.7850 0.1960 31 R 0.0414 0.4362 0.5225 32 N 0.0321 0.1118 0.8561 33 L 0.0548 0.0257 0.9195 34 P 0.0658 0.0451 0.8890 35 R 0.0071 0.8994 0.0936 36 A 0.0048 0.9542 0.0410 37 D 0.0047 0.9603 0.0351 38 L 0.0047 0.9603 0.0350 39 L 0.0047 0.9595 0.0358 40 R 0.0047 0.9601 0.0353 41 E 0.0047 0.9584 0.0369 42 A 0.0047 0.9585 0.0368 43 V 0.0047 0.9596 0.0357 44 D 0.0047 0.9604 0.0349 45 Q 0.0047 0.9585 0.0368 46 Y 0.0048 0.9551 0.0401 47 L 0.0050 0.9452 0.0498 48 I 0.0063 0.9045 0.0892 49 N 0.0201 0.7029 0.2770 50 Q 0.0507 0.3655 0.5838 51 S 0.0442 0.1992 0.7566 52 Q 0.0505 0.3097 0.6397 53 T 0.0699 0.4380 0.4922 54 A 0.0671 0.5594 0.3734 55 R 0.0697 0.5763 0.3540 56 T 0.0808 0.4836 0.4356 57 S 0.0950 0.3084 0.5966 58 V 0.1428 0.1182 0.7390 59 P 0.1170 0.2133 0.6697 60 G 0.2602 0.2332 0.5066 61 I 0.3438 0.2531 0.4031 62 W 0.2996 0.2512 0.4492 63 Q 0.1731 0.1838 0.6430 64 G 0.0858 0.0845 0.8297 65 C 0.1079 0.0638 0.8284 66 E 0.0939 0.1951 0.7110 67 E 0.0669 0.3423 0.5908 68 D 0.0847 0.2852 0.6301 69 G 0.0681 0.5575 0.3744 70 V 0.0228 0.8743 0.1029 71 E 0.0148 0.9146 0.0706 72 Y 0.0111 0.9228 0.0661 73 Q 0.0069 0.9457 0.0474 74 R 0.0051 0.9528 0.0421 75 K 0.0049 0.9408 0.0543 76 L 0.0058 0.9155 0.0787 77 R 0.0064 0.8893 0.1043 78 E 0.0061 0.8115 0.1824 79 E 0.0088 0.7009 0.2903 80 W 0.0257 0.3719 0.6024