# This file is the result of combining several RDB files, specifically # T0377.t06.dssp-ebghstl.rdb (weight 1.53986) # T0377.t06.stride-ebghtl.rdb (weight 1.24869) # T0377.t06.str2.rdb (weight 1.54758) # T0377.t06.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 T0377.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0377 # Using neural net t06-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 T0377.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 82.3526 # # ============================================ # Comments from T0377.t06.stride-ebghtl.rdb # ============================================ # TARGET T0377 # Using neural net t06-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 T0377.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 82.3526 # # ============================================ # Comments from T0377.t06.str2.rdb # ============================================ # TARGET T0377 # Using neural net 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 T0377.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 82.3526 # # ============================================ # Comments from T0377.t06.alpha.rdb # ============================================ # TARGET T0377 # Using neural net 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 T0377.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 82.3526 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1001 0.0438 0.8561 2 A 0.3379 0.0303 0.6318 3 M 0.6269 0.0081 0.3649 4 L 0.8825 0.0036 0.1138 5 Y 0.9302 0.0033 0.0665 6 L 0.9336 0.0032 0.0632 7 I 0.9329 0.0032 0.0639 8 F 0.9215 0.0038 0.0747 9 Y 0.8601 0.0052 0.1348 10 D 0.6077 0.0060 0.3863 11 I 0.1534 0.0371 0.8095 12 T 0.0691 0.0564 0.8744 13 D 0.0490 0.2369 0.7141 14 D 0.0106 0.7616 0.2278 15 N 0.0100 0.8736 0.1164 16 L 0.0074 0.9298 0.0628 17 R 0.0052 0.9472 0.0476 18 N 0.0050 0.9490 0.0460 19 R 0.0047 0.9555 0.0398 20 V 0.0047 0.9582 0.0371 21 A 0.0047 0.9609 0.0344 22 E 0.0046 0.9614 0.0340 23 F 0.0046 0.9608 0.0346 24 L 0.0047 0.9574 0.0379 25 K 0.0049 0.9441 0.0510 26 K 0.0072 0.8761 0.1167 27 K 0.0387 0.5666 0.3947 28 G 0.0313 0.1339 0.8348 29 L 0.0710 0.1306 0.7984 30 D 0.1079 0.3037 0.5884 31 R 0.2641 0.4429 0.2931 32 I 0.3662 0.3702 0.2637 33 Q 0.4456 0.2945 0.2599 34 Y 0.4258 0.1784 0.3958 35 S 0.5401 0.0907 0.3693 36 V 0.6018 0.1121 0.2860 37 F 0.6874 0.0864 0.2262 38 M 0.7472 0.0708 0.1821 39 G 0.7165 0.0334 0.2501 40 D 0.6521 0.0216 0.3263 41 L 0.3650 0.0258 0.6092 42 N 0.0990 0.0174 0.8836 43 S 0.0054 0.8974 0.0972 44 S 0.0050 0.9219 0.0730 45 R 0.0050 0.9381 0.0570 46 L 0.0052 0.9534 0.0414 47 K 0.0047 0.9571 0.0382 48 D 0.0050 0.9549 0.0401 49 V 0.0050 0.9538 0.0411 50 E 0.0050 0.9565 0.0386 51 A 0.0052 0.9404 0.0544 52 G 0.0057 0.9015 0.0928 53 L 0.0128 0.8874 0.0998 54 K 0.0313 0.8366 0.1322 55 I 0.0522 0.8107 0.1372 56 I 0.0705 0.7263 0.2033 57 G 0.0939 0.5244 0.3817 58 N 0.0971 0.3766 0.5262 59 R 0.1284 0.3864 0.4853 60 K 0.1531 0.4242 0.4227 61 K 0.2092 0.3436 0.4472 62 L 0.2544 0.3359 0.4098 63 Q 0.2875 0.2052 0.5073 64 E 0.1744 0.1021 0.7235 65 D 0.0623 0.1869 0.7508 66 E 0.1100 0.1768 0.7132 67 R 0.3519 0.0959 0.5522 68 F 0.5126 0.0249 0.4625 69 F 0.8399 0.0067 0.1534 70 I 0.9204 0.0034 0.0763 71 L 0.9245 0.0038 0.0718 72 I 0.9231 0.0033 0.0736 73 V 0.8680 0.0057 0.1263 74 P 0.7414 0.0056 0.2530 75 I 0.3027 0.0206 0.6767 76 T 0.1245 0.0209 0.8546 77 E 0.0151 0.5419 0.4430 78 N 0.0215 0.5455 0.4331 79 Q 0.0561 0.5893 0.3546 80 F 0.2033 0.4138 0.3829 81 R 0.3204 0.2854 0.3942 82 E 0.5166 0.2078 0.2755 83 R 0.6847 0.1574 0.1579 84 I 0.7861 0.1113 0.1026 85 V 0.7775 0.1192 0.1033 86 I 0.5883 0.1341 0.2776 87 G 0.2942 0.0493 0.6564 88 Y 0.1784 0.0556 0.7660 89 S 0.1280 0.0720 0.8001 90 G 0.0873 0.0805 0.8322 91 S 0.1058 0.1054 0.7889 92 E 0.1183 0.2301 0.6516 93 R 0.1206 0.2842 0.5952 94 E 0.1241 0.3132 0.5627 95 E 0.1485 0.2381 0.6134 96 K 0.1743 0.1527 0.6730 97 S 0.2159 0.1001 0.6841 98 N 0.5130 0.0562 0.4309 99 V 0.7619 0.0269 0.2112 100 V 0.6424 0.0223 0.3352 101 W 0.2047 0.0184 0.7769