# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1034 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1034 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1034 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1034 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0727 0.0133 0.9140 2 S 0.1041 0.0295 0.8664 3 D 0.0812 0.1081 0.8107 4 N 0.0535 0.1799 0.7666 5 S 0.0503 0.1805 0.7692 6 K 0.0841 0.0641 0.8518 7 T 0.2156 0.0390 0.7454 8 R 0.7982 0.0047 0.1971 9 V 0.9235 0.0034 0.0731 10 V 0.9339 0.0032 0.0629 11 V 0.9307 0.0035 0.0658 12 G 0.9199 0.0048 0.0753 13 M 0.8542 0.0084 0.1374 14 S 0.4913 0.0205 0.4882 15 G 0.1176 0.0313 0.8511 16 G 0.0782 0.0664 0.8554 17 V 0.0655 0.3305 0.6040 18 D 0.0355 0.5558 0.4086 19 S 0.0067 0.9108 0.0826 20 S 0.0053 0.9528 0.0419 21 V 0.0047 0.9593 0.0360 22 T 0.0049 0.9603 0.0348 23 A 0.0047 0.9607 0.0347 24 L 0.0047 0.9605 0.0348 25 L 0.0047 0.9607 0.0346 26 L 0.0047 0.9592 0.0361 27 K 0.0048 0.9515 0.0436 28 E 0.0058 0.9017 0.0925 29 Q 0.0412 0.3781 0.5807 30 G 0.0368 0.0181 0.9451 31 Y 0.0851 0.0099 0.9050 32 D 0.4503 0.0079 0.5418 33 V 0.8559 0.0031 0.1410 34 I 0.8897 0.0064 0.1039 35 G 0.9294 0.0035 0.0670 36 I 0.9305 0.0033 0.0662 37 F 0.9232 0.0035 0.0733 38 M 0.8671 0.0067 0.1263 39 K 0.6764 0.0241 0.2995 40 N 0.4864 0.0176 0.4961 41 W 0.2221 0.0527 0.7252 42 D 0.1410 0.0692 0.7898 43 D 0.0982 0.1099 0.7919 44 T 0.0981 0.1149 0.7869 45 D 0.0872 0.1014 0.8114 46 E 0.1147 0.1356 0.7497 47 N 0.1008 0.1182 0.7810 48 G 0.0942 0.0827 0.8231 49 V 0.2184 0.0808 0.7008 50 C 0.2598 0.0627 0.6775 51 T 0.1265 0.0599 0.8136 52 A 0.0740 0.1326 0.7934 53 T 0.0347 0.4252 0.5400 54 E 0.0527 0.4776 0.4697 55 D 0.0615 0.4683 0.4702 56 Y 0.0070 0.9034 0.0896 57 K 0.0055 0.9323 0.0622 58 D 0.0049 0.9424 0.0527 59 V 0.0047 0.9570 0.0383 60 V 0.0046 0.9611 0.0343 61 A 0.0046 0.9603 0.0351 62 V 0.0047 0.9607 0.0346 63 A 0.0047 0.9603 0.0350 64 D 0.0048 0.9530 0.0422 65 Q 0.0054 0.9327 0.0619 66 I 0.0443 0.4953 0.4604 67 G 0.0428 0.0148 0.9424 68 I 0.0642 0.0077 0.9281 69 P 0.2692 0.0121 0.7187 70 Y 0.8457 0.0058 0.1485 71 Y 0.9103 0.0044 0.0853 72 S 0.9207 0.0039 0.0754 73 V 0.8433 0.0095 0.1472 74 N 0.5001 0.0067 0.4932 75 F 0.0823 0.3093 0.6084 76 E 0.0256 0.5981 0.3762 77 K 0.0093 0.8482 0.1425 78 E 0.0104 0.8848 0.1048 79 Y 0.0098 0.8939 0.0963 80 W 0.0066 0.9238 0.0696 81 D 0.0064 0.9257 0.0679 82 R 0.0076 0.9182 0.0742 83 V 0.0097 0.9185 0.0718 84 F 0.0109 0.9231 0.0660 85 E 0.0076 0.9370 0.0554 86 Y 0.0071 0.9418 0.0511 87 F 0.0060 0.9390 0.0550 88 L 0.0068 0.9387 0.0545 89 A 0.0056 0.9402 0.0542 90 E 0.0067 0.9341 0.0592 91 Y 0.0101 0.9139 0.0760 92 R 0.0148 0.8503 0.1349 93 A 0.0400 0.4017 0.5582 94 G 0.0285 0.0556 0.9159 95 R 0.0831 0.0313 0.8855 96 T 0.1503 0.0176 0.8321 97 P 0.1279 0.0296 0.8425 98 N 0.1147 0.0221 0.8632 99 P 0.0519 0.1964 0.7517 100 D 0.0860 0.2626 0.6514 101 V 0.0739 0.5208 0.4053 102 M 0.0886 0.4570 0.4545 103 C 0.0625 0.4896 0.4479 104 N 0.0395 0.4530 0.5075 105 K 0.0149 0.7844 0.2008 106 E 0.0182 0.8587 0.1231 107 I 0.0363 0.8418 0.1219 108 K 0.0278 0.8428 0.1294 109 F 0.0068 0.9339 0.0593 110 K 0.0054 0.9500 0.0446 111 A 0.0049 0.9553 0.0398 112 F 0.0048 0.9568 0.0385 113 L 0.0047 0.9605 0.0349 114 D 0.0047 0.9604 0.0349 115 Y 0.0047 0.9603 0.0351 116 A 0.0047 0.9603 0.0350 117 I 0.0048 0.9537 0.0416 118 T 0.0051 0.9307 0.0643 119 L 0.0429 0.4257 0.5314 120 G 0.0514 0.0113 0.9372 121 A 0.0829 0.0075 0.9096 122 D 0.0765 0.0523 0.8711 123 Y 0.8886 0.0063 0.1051 124 V 0.9258 0.0051 0.0691 125 A 0.9116 0.0094 0.0790 126 T 0.8036 0.0203 0.1761 127 G 0.3622 0.0374 0.6004 128 H 0.2214 0.1124 0.6662 129 Y 0.1691 0.2187 0.6122 130 A 0.1609 0.3898 0.4492 131 R 0.1535 0.4485 0.3980 132 V 0.1912 0.4502 0.3586 133 A 0.2006 0.4302 0.3692 134 R 0.1608 0.3612 0.4780 135 D 0.1070 0.2187 0.6743 136 E 0.0698 0.0954 0.8348 137 D 0.0592 0.0186 0.9222