# This file is the result of combining several RDB files, specifically # T0482.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0482.t2k.stride-ebghtl.rdb (weight 1.24869) # T0482.t2k.str.rdb (weight 1.53983) # 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 T0482.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0482 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0482.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13 # # ============================================ # Comments from T0482.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0482 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0482.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13 # # ============================================ # Comments from T0482.t2k.str.rdb # ============================================ # TARGET T0482 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0482.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0183 0.0076 0.9741 2 F 0.1385 0.0145 0.8470 3 E 0.1295 0.0189 0.8515 4 P 0.1258 0.0393 0.8349 5 G 0.2623 0.0463 0.6914 6 H 0.6830 0.0305 0.2865 7 L 0.7602 0.0371 0.2027 8 H 0.7721 0.0467 0.1813 9 L 0.6077 0.0946 0.2977 10 V 0.4533 0.0880 0.4587 11 S 0.3012 0.0975 0.6013 12 L 0.1681 0.0576 0.7744 13 P 0.0850 0.0740 0.8411 14 G 0.0470 0.0765 0.8765 15 L 0.0350 0.1283 0.8368 16 D 0.0333 0.1060 0.8607 17 Q 0.0671 0.0864 0.8465 18 Q 0.1332 0.0446 0.8222 19 D 0.2556 0.0234 0.7209 20 I 0.6237 0.0110 0.3653 21 N 0.7719 0.0056 0.2226 22 I 0.8970 0.0053 0.0976 23 H 0.9216 0.0038 0.0745 24 I 0.9315 0.0038 0.0647 25 R 0.9237 0.0032 0.0732 26 Y 0.8682 0.0071 0.1246 27 E 0.7942 0.0153 0.1905 28 V 0.7032 0.0301 0.2666 29 R 0.5818 0.0375 0.3806 30 Q 0.3649 0.0331 0.6020 31 N 0.1294 0.0221 0.8485 32 A 0.0299 0.1713 0.7988 33 E 0.0245 0.1856 0.7899 34 S 0.0568 0.1701 0.7732 35 G 0.1123 0.0245 0.8632 36 A 0.3843 0.0124 0.6033 37 Y 0.8870 0.0058 0.1072 38 V 0.9327 0.0038 0.0634 39 H 0.9632 0.0027 0.0340 40 F 0.9541 0.0028 0.0432 41 D 0.9366 0.0028 0.0606 42 M 0.9479 0.0025 0.0496 43 D 0.9475 0.0026 0.0499 44 G 0.9397 0.0029 0.0574 45 E 0.9210 0.0040 0.0750 46 I 0.8222 0.0076 0.1702 47 D 0.1335 0.0170 0.8495 48 G 0.0735 0.0163 0.9102 49 K 0.3797 0.0099 0.6104 50 P 0.4872 0.0111 0.5016 51 F 0.3391 0.0682 0.5927 52 S 0.2918 0.1279 0.5803 53 D 0.3114 0.1688 0.5198 54 S 0.3794 0.0937 0.5269 55 F 0.5220 0.0597 0.4184 56 E 0.5305 0.0481 0.4214 57 L 0.2414 0.0401 0.7185 58 P 0.0941 0.1254 0.7805 59 R 0.0155 0.6308 0.3537 60 D 0.0115 0.7172 0.2713 61 T 0.0173 0.7948 0.1879 62 A 0.0262 0.7808 0.1930 63 F 0.0188 0.8240 0.1572 64 N 0.0166 0.8054 0.1780 65 F 0.0054 0.8760 0.1185 66 A 0.0038 0.9384 0.0577 67 S 0.0038 0.9446 0.0516 68 D 0.0038 0.9506 0.0457 69 A 0.0037 0.9652 0.0310 70 T 0.0037 0.9682 0.0281 71 R 0.0037 0.9675 0.0288 72 V 0.0037 0.9700 0.0263 73 A 0.0037 0.9686 0.0276 74 Q 0.0037 0.9604 0.0359 75 K 0.0038 0.9039 0.0923 76 H 0.0047 0.6049 0.3904 77 G 0.0146 0.0626 0.9228 78 L 0.0364 0.0277 0.9359 79 H 0.0316 0.0406 0.9279 80 P 0.0191 0.2049 0.7760 81 K 0.0200 0.2257 0.7542 82 F 0.0287 0.3160 0.6553 83 G 0.0370 0.3465 0.6165 84 A 0.0591 0.4123 0.5287 85 I 0.0776 0.4563 0.4661 86 T 0.0680 0.5123 0.4197 87 R 0.0668 0.5586 0.3746 88 V 0.0326 0.6794 0.2880 89 H 0.0264 0.6787 0.2949 90 K 0.0156 0.7563 0.2282 91 E 0.0130 0.7643 0.2227 92 Y 0.0095 0.8194 0.1711 93 D 0.0062 0.8724 0.1214 94 A 0.0042 0.8834 0.1124 95 M 0.0044 0.8838 0.1118 96 F 0.0041 0.9241 0.0719 97 E 0.0048 0.9378 0.0574 98 D 0.0048 0.9054 0.0898 99 I 0.0037 0.9473 0.0490 100 R 0.0038 0.9581 0.0381 101 A 0.0041 0.9312 0.0647 102 K 0.0043 0.8965 0.0991 103 L 0.0097 0.5952 0.3950 104 H 0.0166 0.0719 0.9115 105 A 0.0386 0.0150 0.9464 106 H 0.0345 0.0193 0.9462 107 P 0.0199 0.0523 0.9278 108 G 0.0200 0.0435 0.9365 109 E 0.1259 0.0176 0.8565 110 P 0.4380 0.0092 0.5528 111 V 0.4678 0.0086 0.5235 112 D 0.1832 0.0213 0.7955 113 L 0.0087 0.7624 0.2289 114 E 0.0077 0.8143 0.1780 115 R 0.0146 0.8692 0.1162 116 I 0.0750 0.6569 0.2680 117 I 0.2019 0.4517 0.3464 118 R 0.2244 0.3231 0.4525 119 H 0.0759 0.1711 0.7530 120 E 0.0105 0.0080 0.9815