# This file is the result of combining several RDB files, specifically # T0207.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0207.t2k.stride-ebghtl.rdb (weight 1.24869) # T0207.t2k.str2.rdb (weight 1.54758) # T0207.t2k.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 T0207.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0207 # 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 T0207.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 49 # # ============================================ # Comments from T0207.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0207 # 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 T0207.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 49 # # ============================================ # Comments from T0207.t2k.str2.rdb # ============================================ # TARGET T0207 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0207.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 49 # # ============================================ # Comments from T0207.t2k.alpha.rdb # ============================================ # TARGET T0207 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0207.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 49 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2100 0.0096 0.7805 2 A 0.6541 0.0040 0.3418 3 L 0.8700 0.0036 0.1264 4 T 0.9088 0.0043 0.0868 5 L 0.9125 0.0036 0.0840 6 Y 0.8049 0.0094 0.1856 7 Q 0.4968 0.0118 0.4915 8 R 0.1014 0.0220 0.8766 9 D 0.0255 0.0852 0.8893 10 D 0.0294 0.0774 0.8932 11 C 0.0842 0.0931 0.8227 12 H 0.0817 0.3326 0.5857 13 L 0.0587 0.6119 0.3294 14 C 0.0162 0.8600 0.1237 15 D 0.0055 0.9438 0.0507 16 Q 0.0051 0.9501 0.0448 17 A 0.0047 0.9543 0.0409 18 V 0.0050 0.9547 0.0403 19 E 0.0049 0.9470 0.0481 20 A 0.0053 0.9191 0.0756 21 L 0.0083 0.8870 0.1046 22 A 0.0100 0.8466 0.1434 23 Q 0.0132 0.7393 0.2475 24 A 0.0325 0.5050 0.4625 25 R 0.0812 0.3211 0.5977 26 A 0.1138 0.1462 0.7400 27 G 0.1759 0.0348 0.7892 28 A 0.4071 0.0137 0.5792 29 F 0.7145 0.0079 0.2776 30 F 0.8527 0.0065 0.1408 31 S 0.8988 0.0045 0.0967 32 V 0.8343 0.0099 0.1558 33 F 0.6899 0.0099 0.3001 34 I 0.2312 0.1048 0.6640 35 D 0.0910 0.0864 0.8226 36 D 0.0597 0.0612 0.8792 37 D 0.0841 0.0413 0.8746 38 A 0.0055 0.9022 0.0923 39 A 0.0052 0.9308 0.0640 40 L 0.0051 0.9400 0.0549 41 E 0.0056 0.9386 0.0558 42 S 0.0071 0.9123 0.0806 43 A 0.0102 0.8290 0.1608 44 Y 0.0473 0.5555 0.3973 45 G 0.0412 0.2290 0.7298 46 L 0.1244 0.1817 0.6939 47 R 0.2692 0.0975 0.6333 48 V 0.4803 0.0206 0.4990 49 P 0.5867 0.0089 0.4045 50 V 0.8438 0.0064 0.1498 51 L 0.8885 0.0059 0.1056 52 R 0.8321 0.0069 0.1610 53 D 0.5554 0.0185 0.4261 54 P 0.0775 0.0440 0.8785 55 M 0.0329 0.0833 0.8838 56 G 0.2479 0.1113 0.6408 57 R 0.6116 0.0884 0.3000 58 E 0.6409 0.0828 0.2763 59 L 0.5743 0.1098 0.3159 60 D 0.3958 0.0899 0.5143 61 W 0.3179 0.0445 0.6376 62 P 0.2986 0.0323 0.6691 63 F 0.2286 0.0288 0.7427 64 D 0.1192 0.0226 0.8582 65 A 0.0060 0.9064 0.0876 66 P 0.0049 0.9450 0.0501 67 R 0.0048 0.9525 0.0428 68 L 0.0047 0.9564 0.0389 69 R 0.0048 0.9533 0.0419 70 A 0.0050 0.9440 0.0510 71 W 0.0063 0.9107 0.0831 72 L 0.0204 0.8397 0.1400 73 D 0.0116 0.6413 0.3472 74 A 0.0241 0.4389 0.5370 75 A 0.0636 0.1823 0.7541 76 P 0.0426 0.1654 0.7921 77 H 0.0515 0.1333 0.8151 78 A 0.0369 0.0467 0.9164