# This file is the result of combining several RDB files, specifically # T0467.t04.dssp-ebghstl.rdb (weight 1.53986) # T0467.t04.stride-ebghtl.rdb (weight 1.24869) # T0467.t04.str2.rdb (weight 1.54758) # T0467.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 T0467.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.stride-ebghtl.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ # Comments from T0467.t04.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.4357 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1099 0.0501 0.8400 2 D 0.1817 0.0714 0.7469 3 L 0.2056 0.1447 0.6497 4 N 0.1943 0.1168 0.6889 5 R 0.1233 0.2234 0.6533 6 M 0.1496 0.1380 0.7124 7 G 0.2170 0.0730 0.7100 8 K 0.1830 0.0582 0.7588 9 D 0.3339 0.0350 0.6311 10 E 0.7159 0.0141 0.2700 11 Y 0.8903 0.0040 0.1057 12 Y 0.9206 0.0033 0.0760 13 V 0.9225 0.0036 0.0739 14 Q 0.9235 0.0038 0.0727 15 I 0.9156 0.0045 0.0799 16 T 0.7969 0.0064 0.1967 17 V 0.3226 0.0701 0.6073 18 D 0.0790 0.0405 0.8805 19 G 0.0760 0.0410 0.8830 20 K 0.6122 0.0196 0.3682 21 E 0.8655 0.0099 0.1246 22 V 0.8133 0.0166 0.1702 23 H 0.7840 0.0184 0.1977 24 S 0.7441 0.0213 0.2345 25 K 0.7123 0.0310 0.2567 26 A 0.4165 0.0795 0.5039 27 D 0.1994 0.1086 0.6920 28 N 0.0695 0.0548 0.8757 29 G 0.0766 0.0418 0.8816 30 Q 0.2886 0.0283 0.6831 31 K 0.6816 0.0186 0.2998 32 Y 0.6923 0.0190 0.2887 33 K 0.6519 0.0371 0.3110 34 D 0.6755 0.0195 0.3050 35 Y 0.7964 0.0084 0.1953 36 E 0.8782 0.0058 0.1159 37 Y 0.9064 0.0041 0.0895 38 K 0.9002 0.0035 0.0963 39 L 0.8686 0.0033 0.1280 40 T 0.8356 0.0067 0.1577 41 G 0.8813 0.0051 0.1136 42 F 0.8622 0.0066 0.1311 43 D 0.4194 0.0135 0.5671 44 K 0.0255 0.1167 0.8578 45 D 0.0468 0.0252 0.9280 46 G 0.0774 0.0306 0.8920 47 K 0.3350 0.0115 0.6535 48 E 0.8659 0.0040 0.1301 49 K 0.8908 0.0055 0.1036 50 E 0.9239 0.0035 0.0726 51 L 0.9186 0.0037 0.0777 52 E 0.9179 0.0039 0.0782 53 F 0.8724 0.0071 0.1206 54 T 0.6533 0.0178 0.3289 55 A 0.3362 0.0738 0.5899 56 Q 0.1509 0.1757 0.6734 57 K 0.0825 0.2737 0.6438 58 N 0.0997 0.2626 0.6377 59 L 0.1699 0.1638 0.6662 60 R 0.1347 0.1032 0.7620 61 K 0.0896 0.3552 0.5552 62 E 0.1031 0.1688 0.7281 63 A 0.4039 0.0726 0.5235 64 F 0.7875 0.0119 0.2006 65 L 0.8832 0.0070 0.1098 66 R 0.9236 0.0050 0.0714 67 V 0.9232 0.0046 0.0722 68 Y 0.9070 0.0058 0.0873 69 H 0.8291 0.0088 0.1621 70 S 0.2933 0.0446 0.6622 71 D 0.0547 0.0906 0.8546 72 K 0.0646 0.1141 0.8213 73 K 0.1268 0.0569 0.8163 74 G 0.3506 0.0409 0.6085 75 V 0.6754 0.0124 0.3123 76 S 0.6387 0.0386 0.3227 77 A 0.5401 0.0153 0.4447 78 W 0.2557 0.4563 0.2880 79 E 0.3054 0.4512 0.2434 80 E 0.4115 0.3326 0.2559 81 V 0.4855 0.1194 0.3951 82 K 0.2730 0.1062 0.6209 83 K 0.0090 0.8583 0.1326 84 D 0.0097 0.7823 0.2080 85 E 0.0144 0.7462 0.2394 86 L 0.0682 0.2506 0.6812 87 P 0.0452 0.3174 0.6374 88 A 0.0049 0.9397 0.0555 89 K 0.0048 0.9465 0.0488 90 V 0.0048 0.9529 0.0423 91 K 0.0048 0.9520 0.0432 92 E 0.0051 0.9380 0.0569 93 K 0.0071 0.8960 0.0970 94 L 0.0481 0.6071 0.3448 95 G 0.0368 0.1047 0.8585 96 V 0.0604 0.0402 0.8994 97 K 0.0595 0.0464 0.8941