# This file is the result of combining several RDB files, specifically # T0372.t06.dssp-ebghstl.rdb (weight 1.53986) # T0372.t06.stride-ebghtl.rdb (weight 1.24869) # T0372.t06.str2.rdb (weight 1.54758) # T0372.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 T0372.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 26 # # ============================================ # Comments from T0372.t06.stride-ebghtl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 26 # # ============================================ # Comments from T0372.t06.str2.rdb # ============================================ # TARGET T0372 # 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 T0372.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 26 # # ============================================ # Comments from T0372.t06.alpha.rdb # ============================================ # TARGET T0372 # 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 T0372.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 26 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0595 0.0283 0.9122 2 I 0.0960 0.0269 0.8771 3 P 0.1154 0.0521 0.8325 4 F 0.1421 0.0616 0.7963 5 K 0.2107 0.0489 0.7405 6 D 0.2477 0.0268 0.7255 7 I 0.2590 0.0094 0.7316 8 T 0.3280 0.0116 0.6604 9 L 0.1287 0.4165 0.4549 10 A 0.0610 0.3505 0.5885 11 D 0.0897 0.2595 0.6508 12 R 0.0120 0.8330 0.1549 13 D 0.0056 0.8972 0.0973 14 T 0.0056 0.9220 0.0723 15 I 0.0080 0.9175 0.0744 16 T 0.0073 0.9271 0.0656 17 A 0.0073 0.9134 0.0793 18 F 0.0090 0.8835 0.1075 19 T 0.0223 0.7756 0.2021 20 M 0.0223 0.6391 0.3386 21 K 0.0299 0.4650 0.5051 22 S 0.0506 0.2286 0.7208 23 D 0.0602 0.1403 0.7994 24 R 0.0829 0.2317 0.6854 25 R 0.1443 0.2585 0.5973 26 N 0.1761 0.2996 0.5244 27 C 0.2058 0.2668 0.5275 28 D 0.1702 0.3866 0.4432 29 L 0.1894 0.4307 0.3799 30 S 0.1768 0.4893 0.3339 31 F 0.1004 0.7193 0.1803 32 S 0.0763 0.7539 0.1697 33 N 0.0699 0.7828 0.1473 34 L 0.0785 0.7918 0.1297 35 C 0.1046 0.7623 0.1331 36 S 0.1493 0.6768 0.1739 37 W 0.1648 0.6059 0.2293 38 R 0.1686 0.5085 0.3229 39 F 0.1854 0.3540 0.4607 40 L 0.2687 0.2393 0.4920 41 Y 0.2640 0.1294 0.6067 42 D 0.2678 0.0558 0.6763 43 T 0.6319 0.0200 0.3481 44 Q 0.8456 0.0109 0.1435 45 F 0.9001 0.0060 0.0939 46 A 0.9050 0.0049 0.0901 47 V 0.9182 0.0040 0.0779 48 I 0.8079 0.0165 0.1756 49 D 0.2767 0.0525 0.6709 50 D 0.1820 0.0564 0.7616 51 F 0.8326 0.0069 0.1605 52 L 0.9203 0.0032 0.0765 53 V 0.9255 0.0037 0.0708 54 F 0.9228 0.0045 0.0726 55 K 0.8802 0.0194 0.1005 56 F 0.8595 0.0066 0.1339 57 W 0.7222 0.0159 0.2619 58 A 0.4312 0.0401 0.5287 59 G 0.0605 0.0558 0.8837 60 E 0.0831 0.0712 0.8458 61 Q 0.4613 0.0376 0.5011 62 L 0.6860 0.0250 0.2890 63 A 0.8070 0.0245 0.1685 64 Y 0.8509 0.0173 0.1318 65 M 0.7596 0.0166 0.2239 66 M 0.4962 0.0236 0.4802 67 P 0.2983 0.0345 0.6672 68 V 0.1717 0.0580 0.7703 69 G 0.0943 0.0427 0.8630 70 N 0.0420 0.1805 0.7775 71 G 0.0445 0.1614 0.7941 72 D 0.1008 0.1630 0.7362 73 L 0.0057 0.9240 0.0704 74 K 0.0047 0.9561 0.0392 75 A 0.0047 0.9597 0.0357 76 V 0.0047 0.9603 0.0350 77 L 0.0047 0.9602 0.0351 78 R 0.0047 0.9606 0.0347 79 K 0.0047 0.9566 0.0387 80 L 0.0048 0.9496 0.0456 81 I 0.0051 0.9439 0.0510 82 E 0.0060 0.9299 0.0641 83 D 0.0073 0.8933 0.0994 84 A 0.0070 0.8775 0.1155 85 D 0.0098 0.7991 0.1911 86 K 0.0106 0.7128 0.2765 87 E 0.0339 0.4715 0.4946 88 K 0.0359 0.2068 0.7573 89 H 0.0699 0.1034 0.8267 90 N 0.1280 0.0567 0.8153 91 F 0.4528 0.0197 0.5275 92 C 0.7121 0.0175 0.2704 93 M 0.8039 0.0315 0.1646 94 L 0.6481 0.0916 0.2603 95 G 0.4807 0.0470 0.4722 96 V 0.2564 0.0307 0.7128 97 C 0.1164 0.0436 0.8400 98 S 0.0131 0.7441 0.2428 99 N 0.0101 0.8019 0.1880 100 M 0.0062 0.9042 0.0896 101 R 0.0057 0.9331 0.0612 102 A 0.0051 0.9368 0.0581 103 D 0.0048 0.9417 0.0534 104 L 0.0050 0.9371 0.0579 105 E 0.0061 0.9239 0.0700 106 A 0.0075 0.8749 0.1176 107 I 0.0204 0.6798 0.2998 108 L 0.0704 0.1078 0.8218 109 P 0.0367 0.2283 0.7350 110 E 0.0400 0.2685 0.6914 111 R 0.2608 0.1790 0.5602 112 F 0.6911 0.0159 0.2930 113 I 0.8517 0.0105 0.1378 114 F 0.8662 0.0064 0.1274 115 T 0.7372 0.0155 0.2473 116 E 0.5235 0.0352 0.4413 117 D 0.2918 0.0472 0.6609 118 R 0.0970 0.3220 0.5810 119 A 0.0716 0.3074 0.6210 120 Y 0.0900 0.3029 0.6072 121 A 0.1003 0.1647 0.7350 122 D 0.0984 0.0835 0.8182