# This file is the result of combining several RDB files, specifically # T0408.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0408.t2k.stride-ebghtl.rdb (weight 1.24869) # T0408.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 T0408.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 332 # # ============================================ # Comments from T0408.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 332 # # ============================================ # Comments from T0408.t2k.str.rdb # ============================================ # TARGET T0408 # 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 T0408.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 332 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0230 0.0177 0.9593 2 K 0.1592 0.0798 0.7610 3 N 0.1441 0.1867 0.6692 4 E 0.0808 0.4183 0.5009 5 V 0.0575 0.4616 0.4809 6 F 0.0810 0.4802 0.4388 7 F 0.0371 0.5906 0.3723 8 G 0.0108 0.8547 0.1345 9 E 0.0078 0.9151 0.0771 10 G 0.0059 0.9372 0.0569 11 M 0.0059 0.9430 0.0511 12 K 0.0051 0.9430 0.0518 13 V 0.0048 0.9362 0.0591 14 V 0.0043 0.9272 0.0685 15 K 0.0045 0.8872 0.1083 16 E 0.0043 0.8114 0.1843 17 K 0.0046 0.7677 0.2277 18 Y 0.0087 0.2990 0.6924 19 P 0.0046 0.8352 0.1602 20 D 0.0040 0.8736 0.1224 21 L 0.0038 0.9472 0.0489 22 Y 0.0041 0.9653 0.0307 23 D 0.0045 0.9680 0.0275 24 I 0.0041 0.9685 0.0274 25 I 0.0042 0.9670 0.0289 26 V 0.0044 0.9584 0.0372 27 K 0.0045 0.9301 0.0654 28 L 0.0062 0.8791 0.1147 29 N 0.0101 0.7788 0.2112 30 D 0.0169 0.7030 0.2801 31 T 0.0338 0.6988 0.2674 32 V 0.0735 0.6122 0.3143 33 F 0.0957 0.4722 0.4321 34 T 0.0690 0.2583 0.6727 35 G 0.0300 0.1768 0.7932 36 K 0.0241 0.1130 0.8630 37 T 0.0568 0.1064 0.8368 38 L 0.0722 0.0644 0.8634 39 D 0.0206 0.0680 0.9114 40 Y 0.0041 0.9238 0.0720 41 K 0.0040 0.9483 0.0477 42 T 0.0038 0.9705 0.0257 43 Q 0.0037 0.9748 0.0215 44 K 0.0037 0.9750 0.0213 45 L 0.0037 0.9766 0.0197 46 I 0.0037 0.9770 0.0193 47 A 0.0037 0.9766 0.0197 48 I 0.0037 0.9770 0.0193 49 G 0.0037 0.9770 0.0193 50 I 0.0037 0.9770 0.0193 51 V 0.0037 0.9755 0.0208 52 A 0.0037 0.9652 0.0311 53 S 0.0038 0.9054 0.0908 54 R 0.0041 0.6315 0.3645 55 C 0.0138 0.1716 0.8146 56 D 0.0126 0.0931 0.8943 57 E 0.0044 0.8594 0.1362 58 V 0.0040 0.9165 0.0795 59 A 0.0038 0.9527 0.0434 60 I 0.0041 0.9669 0.0291 61 E 0.0037 0.9729 0.0233 62 K 0.0037 0.9745 0.0217 63 Q 0.0037 0.9737 0.0225 64 M 0.0037 0.9741 0.0222 65 K 0.0037 0.9740 0.0223 66 S 0.0037 0.9728 0.0235 67 A 0.0037 0.9736 0.0227 68 M 0.0037 0.9731 0.0231 69 K 0.0037 0.9687 0.0275 70 E 0.0039 0.8912 0.1049 71 L 0.0049 0.3454 0.6498 72 G 0.0093 0.0105 0.9802 73 I 0.0159 0.0052 0.9789 74 T 0.0187 0.0098 0.9715 75 K 0.0040 0.9294 0.0666 76 E 0.0039 0.9580 0.0381 77 E 0.0037 0.9720 0.0242 78 I 0.0037 0.9759 0.0204 79 A 0.0037 0.9759 0.0204 80 D 0.0037 0.9742 0.0221 81 V 0.0037 0.9746 0.0217 82 L 0.0037 0.9755 0.0207 83 R 0.0037 0.9759 0.0204 84 V 0.0037 0.9766 0.0197 85 V 0.0037 0.9763 0.0200 86 L 0.0037 0.9742 0.0221 87 L 0.0037 0.9663 0.0299 88 T 0.0038 0.9039 0.0923 89 S 0.0041 0.7583 0.2376 90 G 0.0062 0.6317 0.3621 91 M 0.0070 0.7712 0.2218 92 P 0.0038 0.9677 0.0285 93 A 0.0037 0.9726 0.0237 94 F 0.0037 0.9745 0.0218 95 T 0.0037 0.9744 0.0219 96 K 0.0037 0.9715 0.0247 97 A 0.0037 0.9716 0.0246 98 M 0.0038 0.9696 0.0267 99 K 0.0038 0.9587 0.0375 100 I 0.0038 0.9462 0.0500 101 L 0.0038 0.9172 0.0791 102 E 0.0047 0.7942 0.2012 103 K 0.0076 0.5907 0.4018 104 L 0.0090 0.0536 0.9373