# This file is the result of combining several RDB files, specifically # T0206.t04.dssp-ebghstl.rdb (weight 1.53986) # T0206.t04.stride-ebghtl.rdb (weight 1.24869) # T0206.t04.str2.rdb (weight 1.54758) # T0206.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 T0206.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0206 # 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 T0206.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 11.9415 # # ============================================ # Comments from T0206.t04.stride-ebghtl.rdb # ============================================ # TARGET T0206 # 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 T0206.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 11.9415 # # ============================================ # Comments from T0206.t04.str2.rdb # ============================================ # TARGET T0206 # 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 T0206.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 11.9415 # # ============================================ # Comments from T0206.t04.alpha.rdb # ============================================ # TARGET T0206 # 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 T0206.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 11.9415 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1608 0.0721 0.7671 2 A 0.2481 0.0819 0.6700 3 F 0.2231 0.0733 0.7036 4 D 0.1211 0.0324 0.8465 5 P 0.0194 0.2718 0.7087 6 N 0.0343 0.2284 0.7373 7 L 0.1340 0.2084 0.6577 8 V 0.2018 0.0993 0.6988 9 G 0.1190 0.0566 0.8243 10 P 0.0983 0.0756 0.8262 11 T 0.1445 0.0659 0.7896 12 L 0.1195 0.0302 0.8503 13 P 0.0985 0.0266 0.8749 14 P 0.1258 0.0364 0.8378 15 I 0.1277 0.0291 0.8431 16 P 0.1086 0.0382 0.8532 17 P 0.1092 0.0834 0.8074 18 F 0.1988 0.0617 0.7395 19 T 0.2523 0.0479 0.6997 20 L 0.1795 0.0230 0.7976 21 P 0.1635 0.0453 0.7912 22 T 0.2275 0.0489 0.7236 23 G 0.1350 0.0368 0.8283 24 P 0.1095 0.0756 0.8149 25 T 0.2076 0.0593 0.7331 26 G 0.1251 0.0389 0.8360 27 P 0.1082 0.0809 0.8109 28 T 0.1945 0.0707 0.7348 29 G 0.1258 0.0475 0.8267 30 P 0.1121 0.0933 0.7946 31 T 0.2100 0.0783 0.7117 32 G 0.1194 0.0538 0.8268 33 P 0.0939 0.1001 0.8060 34 T 0.1774 0.0806 0.7420 35 G 0.1167 0.0432 0.8400 36 P 0.1097 0.0871 0.8032 37 T 0.2071 0.0662 0.7268 38 G 0.1428 0.0385 0.8188 39 P 0.1427 0.0623 0.7950 40 T 0.2302 0.0693 0.7006 41 G 0.1439 0.0704 0.7857 42 P 0.1350 0.1243 0.7407 43 T 0.2401 0.0994 0.6605 44 G 0.1428 0.0942 0.7630 45 D 0.1172 0.1326 0.7502 46 T 0.1791 0.1229 0.6980 47 G 0.1606 0.0771 0.7624 48 T 0.1966 0.0798 0.7236 49 T 0.2761 0.0598 0.6641 50 G 0.1684 0.0316 0.8000 51 P 0.1463 0.0592 0.7945 52 T 0.2015 0.0630 0.7355 53 G 0.1261 0.0464 0.8275 54 P 0.1171 0.0856 0.7972 55 T 0.2005 0.0681 0.7314 56 G 0.1336 0.0471 0.8193 57 P 0.1151 0.0888 0.7961 58 T 0.2079 0.0699 0.7222 59 G 0.1361 0.0539 0.8099 60 P 0.1162 0.0895 0.7944 61 T 0.2031 0.0780 0.7189 62 G 0.1175 0.0647 0.8178 63 P 0.1065 0.1449 0.7486 64 T 0.1926 0.1344 0.6730 65 G 0.1748 0.1169 0.7083 66 A 0.1712 0.1401 0.6888 67 T 0.2377 0.1191 0.6432 68 G 0.1819 0.0661 0.7521 69 L 0.1866 0.0766 0.7368 70 T 0.2262 0.0707 0.7031 71 G 0.1327 0.0484 0.8189 72 P 0.1060 0.0936 0.8003 73 T 0.1813 0.0769 0.7418 74 G 0.1250 0.0567 0.8183 75 P 0.1139 0.0887 0.7974 76 T 0.1898 0.0849 0.7253 77 G 0.1268 0.0606 0.8126 78 P 0.1034 0.1344 0.7622 79 S 0.1531 0.1320 0.7149 80 G 0.1299 0.1098 0.7603 81 L 0.1520 0.1016 0.7464 82 G 0.1908 0.0897 0.7196 83 L 0.1493 0.0651 0.7856 84 P 0.1451 0.1056 0.7493 85 A 0.1698 0.1560 0.6743 86 G 0.1531 0.1299 0.7171 87 L 0.1915 0.1659 0.6426 88 Y 0.2240 0.1540 0.6219 89 A 0.1705 0.0845 0.7449 90 F 0.0906 0.0454 0.8640