# This file is the result of combining several RDB files, specifically # T0397.t04.dssp-ebghstl.rdb (weight 1.53986) # T0397.t04.stride-ebghtl.rdb (weight 1.24869) # T0397.t04.str2.rdb (weight 1.54758) # T0397.t04.alpha.rdb (weight 0.659012) # T0397.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0397.t2k.stride-ebghtl.rdb (weight 1.24869) # T0397.t2k.str2.rdb (weight 1.54758) # T0397.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 T0397.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.stride-ebghtl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 12 # # ============================================ # Comments from T0397.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0397 # 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 T0397.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 12 # # ============================================ # Comments from T0397.t2k.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 12 # # ============================================ # Comments from T0397.t2k.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 12 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0999 0.0275 0.8726 2 K 0.1745 0.0304 0.7951 3 I 0.1610 0.0165 0.8225 4 P 0.1892 0.0247 0.7862 5 K 0.5861 0.0188 0.3951 6 I 0.8442 0.0130 0.1429 7 Y 0.8838 0.0100 0.1061 8 V 0.8466 0.0110 0.1425 9 E 0.6048 0.0331 0.3621 10 G 0.3426 0.0308 0.6266 11 E 0.2808 0.0703 0.6488 12 L 0.1915 0.1065 0.7019 13 N 0.1497 0.1225 0.7278 14 D 0.1033 0.2042 0.6925 15 G 0.1528 0.2032 0.6440 16 D 0.2862 0.1715 0.5424 17 R 0.4490 0.1481 0.4029 18 V 0.6385 0.1265 0.2349 19 A 0.6558 0.1288 0.2154 20 I 0.5874 0.1477 0.2649 21 E 0.4437 0.1455 0.4107 22 K 0.2143 0.1186 0.6671 23 D 0.2201 0.0670 0.7129 24 G 0.5419 0.0396 0.4185 25 N 0.7916 0.0217 0.1867 26 A 0.8768 0.0147 0.1085 27 I 0.8636 0.0217 0.1148 28 I 0.8035 0.0323 0.1643 29 F 0.6266 0.0681 0.3053 30 L 0.3678 0.1622 0.4700 31 E 0.2910 0.2005 0.5085 32 K 0.1802 0.4264 0.3934 33 D 0.1430 0.5307 0.3263 34 E 0.1101 0.5599 0.3301 35 E 0.1007 0.5062 0.3931 36 Y 0.1150 0.3429 0.5420 37 S 0.0977 0.2769 0.6254 38 G 0.0822 0.2034 0.7144 39 N 0.0585 0.1746 0.7668 40 G 0.0702 0.2047 0.7251 41 K 0.2444 0.2658 0.4899 42 L 0.3013 0.3466 0.3521 43 L 0.2120 0.5552 0.2328 44 Y 0.1085 0.7616 0.1300 45 Q 0.0845 0.8088 0.1067 46 V 0.0899 0.8226 0.0875 47 I 0.0683 0.8489 0.0829 48 Y 0.0258 0.9135 0.0607 49 D 0.0105 0.9385 0.0510 50 D 0.0072 0.9369 0.0559 51 L 0.0060 0.9365 0.0575 52 A 0.0065 0.9252 0.0683 53 K 0.0083 0.8796 0.1120 54 Y 0.0152 0.8090 0.1758 55 M 0.0715 0.6324 0.2961 56 S 0.0630 0.4460 0.4910 57 L 0.0420 0.5308 0.4273 58 D 0.0513 0.3681 0.5806 59 T 0.1003 0.3192 0.5805 60 L 0.1986 0.1818 0.6197 61 K 0.2693 0.0951 0.6357 62 K 0.3146 0.0574 0.6280 63 D 0.5615 0.0148 0.4236 64 V 0.8577 0.0048 0.1375 65 L 0.9195 0.0036 0.0769 66 I 0.9073 0.0036 0.0891 67 Q 0.8360 0.0059 0.1581 68 Y 0.4061 0.0087 0.5852 69 P 0.0789 0.0690 0.8520 70 D 0.0561 0.0519 0.8920 71 K 0.0812 0.0926 0.8263 72 H 0.2230 0.0606 0.7164 73 T 0.5626 0.0366 0.4007 74 L 0.7629 0.0140 0.2231 75 T 0.8589 0.0074 0.1337 76 Y 0.8885 0.0053 0.1062 77 L 0.7780 0.0083 0.2137 78 K 0.4100 0.0208 0.5692 79 A 0.0622 0.0668 0.8709 80 G 0.0451 0.0382 0.9168 81 T 0.2872 0.0187 0.6942 82 K 0.7855 0.0050 0.2096 83 L 0.8828 0.0052 0.1120 84 I 0.8935 0.0051 0.1014 85 S 0.9008 0.0039 0.0954 86 V 0.8154 0.0062 0.1784 87 P 0.6817 0.0075 0.3108 88 A 0.5307 0.0415 0.4277 89 E 0.3611 0.0681 0.5708 90 G 0.2393 0.0596 0.7011 91 Y 0.5605 0.0152 0.4243 92 K 0.8060 0.0054 0.1886 93 V 0.8284 0.0041 0.1675 94 Y 0.8343 0.0062 0.1595 95 P 0.8547 0.0042 0.1411 96 I 0.7959 0.0089 0.1952 97 M 0.7420 0.0144 0.2436 98 D 0.5052 0.0240 0.4708 99 F 0.1997 0.1129 0.6874 100 G 0.1016 0.1029 0.7954 101 F 0.1882 0.1423 0.6694 102 R 0.4599 0.1209 0.4192 103 V 0.5413 0.1342 0.3245 104 L 0.3889 0.1408 0.4703 105 K 0.2404 0.1056 0.6540 106 G 0.1514 0.0374 0.8111 107 Y 0.2662 0.0201 0.7137 108 R 0.6348 0.0128 0.3524 109 L 0.8039 0.0129 0.1832 110 A 0.8538 0.0103 0.1359 111 T 0.9025 0.0072 0.0903 112 L 0.8905 0.0086 0.1009 113 E 0.8805 0.0080 0.1115 114 S 0.7102 0.0149 0.2749 115 K 0.3022 0.0350 0.6628 116 K 0.1796 0.0537 0.7667 117 G 0.3681 0.0267 0.6052 118 D 0.6611 0.0092 0.3297 119 L 0.8756 0.0035 0.1209 120 R 0.8803 0.0086 0.1111 121 Y 0.8954 0.0043 0.1003 122 V 0.8464 0.0105 0.1431 123 N 0.7578 0.0110 0.2311 124 S 0.5064 0.0132 0.4804 125 P 0.1790 0.0442 0.7768 126 V 0.1450 0.0396 0.8155 127 S 0.1447 0.0459 0.8094 128 G 0.2992 0.0187 0.6821 129 T 0.8032 0.0043 0.1926 130 V 0.9209 0.0032 0.0759 131 I 0.9241 0.0033 0.0727 132 F 0.9156 0.0035 0.0809 133 M 0.8723 0.0091 0.1186 134 N 0.7018 0.0218 0.2763 135 E 0.4322 0.0255 0.5423 136 I 0.2711 0.0217 0.7072 137 P 0.1585 0.0826 0.7588 138 S 0.0859 0.1062 0.8079 139 E 0.0761 0.0904 0.8335 140 R 0.0789 0.0850 0.8361 141 A 0.0888 0.1122 0.7989 142 N 0.1473 0.0672 0.7855 143 Y 0.5238 0.0160 0.4602 144 V 0.8227 0.0060 0.1712 145 F 0.9046 0.0037 0.0917 146 Y 0.9000 0.0041 0.0960 147 M 0.8480 0.0045 0.1475 148 L 0.6446 0.0079 0.3475 149 E 0.2578 0.0143 0.7279 150 E 0.0479 0.0272 0.9249