# This file is the result of combining several RDB files, specifically # T0330.t06.dssp-ebghstl.rdb (weight 1.53986) # T0330.t06.stride-ebghtl.rdb (weight 1.24869) # T0330.t06.str2.rdb (weight 1.54758) # T0330.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 T0330.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t06.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0874 0.0187 0.8939 2 K 0.1781 0.0382 0.7836 3 V 0.1369 0.3109 0.5522 4 E 0.0738 0.4565 0.4697 5 S 0.0453 0.7194 0.2353 6 M 0.0300 0.8257 0.1444 7 N 0.0179 0.8521 0.1300 8 R 0.0064 0.9299 0.0636 9 R 0.0056 0.9467 0.0477 10 V 0.0058 0.9498 0.0444 11 L 0.0050 0.9501 0.0449 12 A 0.0055 0.9485 0.0461 13 D 0.0055 0.9411 0.0534 14 A 0.0064 0.9265 0.0671 15 L 0.0092 0.9293 0.0614 16 I 0.0157 0.9195 0.0648 17 E 0.0219 0.9000 0.0782 18 V 0.0490 0.8080 0.1430 19 Y 0.1083 0.5082 0.3835 20 G 0.0802 0.1340 0.7859 21 T 0.0930 0.0789 0.8282 22 E 0.0961 0.1031 0.8007 23 G 0.0868 0.0833 0.8298 24 S 0.1386 0.0889 0.7725 25 T 0.1380 0.1467 0.7153 26 G 0.1536 0.1299 0.7165 27 S 0.2118 0.1252 0.6630 28 H 0.2843 0.1017 0.6139 29 D 0.2336 0.1061 0.6602 30 F 0.2006 0.1595 0.6400 31 S 0.1642 0.2057 0.6301 32 G 0.1516 0.2010 0.6474 33 K 0.1219 0.2878 0.5902 34 M 0.1366 0.3011 0.5622 35 D 0.0684 0.3251 0.6065 36 G 0.0408 0.5230 0.4362 37 A 0.1173 0.7070 0.1756 38 I 0.2142 0.7045 0.0813 39 I 0.1662 0.7746 0.0592 40 Y 0.1386 0.8047 0.0567 41 E 0.0790 0.8602 0.0608 42 V 0.0642 0.8583 0.0775 43 L 0.0511 0.8478 0.1010 44 S 0.0307 0.7937 0.1756 45 N 0.0152 0.7163 0.2685 46 V 0.0475 0.4084 0.5440 47 G 0.0405 0.1014 0.8581 48 L 0.0973 0.0813 0.8214 49 E 0.1039 0.1395 0.7566 50 R 0.0276 0.7532 0.2192 51 A 0.0104 0.8648 0.1248 52 E 0.0114 0.8881 0.1005 53 I 0.0088 0.9098 0.0814 54 A 0.0072 0.9100 0.0827 55 D 0.0055 0.9089 0.0856 56 K 0.0060 0.8999 0.0941 57 F 0.0068 0.8991 0.0940 58 D 0.0052 0.9377 0.0571 59 K 0.0049 0.9449 0.0502 60 A 0.0050 0.9441 0.0509 61 K 0.0049 0.9516 0.0435 62 E 0.0048 0.9520 0.0432 63 T 0.0051 0.9503 0.0445 64 Y 0.0048 0.9539 0.0414 65 I 0.0053 0.9576 0.0372 66 A 0.0052 0.9573 0.0375 67 L 0.0055 0.9559 0.0386 68 F 0.0056 0.9492 0.0453 69 R 0.0065 0.9309 0.0626 70 E 0.0099 0.8844 0.1058 71 R 0.0142 0.7418 0.2440 72 A 0.0635 0.5006 0.4360 73 R 0.0712 0.2167 0.7121 74 R 0.0190 0.6529 0.3281 75 E 0.0173 0.5575 0.4252 76 D 0.0446 0.4811 0.4743 77 I 0.2451 0.2230 0.5319 78 T 0.2282 0.1257 0.6461 79 L 0.0969 0.0450 0.8581