# This file is the result of combining several RDB files, specifically # T0255.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0255.t2k.stride-ebghtl.rdb (weight 1.24869) # T0255.t2k.str2.rdb (weight 1.54758) # T0255.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 T0255.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0255 # 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 T0255.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 69 # # ============================================ # Comments from T0255.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0255 # 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 T0255.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 69 # # ============================================ # Comments from T0255.t2k.str2.rdb # ============================================ # TARGET T0255 # 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 T0255.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 69 # # ============================================ # Comments from T0255.t2k.alpha.rdb # ============================================ # TARGET T0255 # 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 T0255.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 69 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0451 0.0695 0.8853 2 N 0.1015 0.1253 0.7731 3 S 0.0881 0.2000 0.7119 4 K 0.1829 0.1763 0.6408 5 N 0.3658 0.0688 0.5654 6 T 0.4074 0.0437 0.5489 7 I 0.5086 0.0523 0.4391 8 C 0.6258 0.0718 0.3024 9 L 0.7187 0.0601 0.2212 10 W 0.7270 0.0354 0.2375 11 Y 0.4370 0.0315 0.5315 12 D 0.1106 0.0427 0.8467 13 S 0.0292 0.1342 0.8366 14 A 0.0465 0.3998 0.5537 15 A 0.0077 0.9287 0.0637 16 L 0.0052 0.9461 0.0486 17 E 0.0066 0.9527 0.0407 18 A 0.0048 0.9545 0.0407 19 A 0.0055 0.9513 0.0432 20 T 0.0064 0.9436 0.0499 21 F 0.0067 0.9362 0.0571 22 Y 0.0114 0.9113 0.0773 23 A 0.0135 0.8777 0.1088 24 E 0.0177 0.7893 0.1931 25 T 0.0490 0.5949 0.3561 26 F 0.1097 0.1584 0.7319 27 P 0.0278 0.1207 0.8515 28 D 0.0414 0.0817 0.8769 29 S 0.1901 0.0943 0.7156 30 A 0.5689 0.0524 0.3787 31 V 0.7724 0.0328 0.1948 32 L 0.7963 0.0314 0.1723 33 A 0.8272 0.0275 0.1453 34 V 0.8298 0.0271 0.1431 35 H 0.7823 0.0270 0.1907 36 R 0.6526 0.0303 0.3171 37 A 0.3542 0.0297 0.6161 38 P 0.1556 0.0852 0.7591 39 G 0.0856 0.1254 0.7889 40 D 0.0995 0.1394 0.7611 41 Y 0.1316 0.1081 0.7603 42 P 0.1427 0.0926 0.7647 43 S 0.1405 0.1162 0.7433 44 G 0.0932 0.0800 0.8268 45 K 0.0911 0.0814 0.8274 46 E 0.0672 0.0917 0.8412 47 G 0.0756 0.0592 0.8652 48 D 0.3578 0.0209 0.6213 49 V 0.7521 0.0042 0.2437 50 L 0.8732 0.0077 0.1191 51 T 0.9151 0.0032 0.0816 52 V 0.9253 0.0034 0.0714 53 E 0.9252 0.0034 0.0714 54 F 0.9201 0.0039 0.0761 55 R 0.9181 0.0033 0.0786 56 V 0.8180 0.0127 0.1694 57 M 0.0912 0.0230 0.8858 58 G 0.0631 0.0370 0.8999 59 I 0.6620 0.0084 0.3296 60 P 0.8447 0.0041 0.1512 61 C 0.8853 0.0086 0.1061 62 L 0.8956 0.0080 0.0964 63 G 0.8319 0.0150 0.1531 64 L 0.6222 0.0335 0.3442 65 N 0.2395 0.0504 0.7101 66 G 0.1072 0.0542 0.8385 67 G 0.1041 0.0644 0.8315 68 P 0.1215 0.1096 0.7688 69 A 0.1481 0.1209 0.7310 70 F 0.2056 0.0706 0.7239 71 R 0.1637 0.0527 0.7836 72 H 0.1573 0.0562 0.7865 73 S 0.1324 0.0473 0.8203 74 E 0.1609 0.0806 0.7585 75 A 0.5495 0.0319 0.4186 76 F 0.8106 0.0076 0.1818 77 S 0.8953 0.0050 0.0998 78 F 0.9106 0.0040 0.0854 79 Q 0.9228 0.0032 0.0740 80 V 0.8996 0.0043 0.0961 81 A 0.8495 0.0047 0.1458 82 T 0.4894 0.0143 0.4962 83 D 0.0662 0.0693 0.8645 84 D 0.0679 0.0227 0.9094 85 Q 0.0052 0.8966 0.0983 86 A 0.0049 0.9399 0.0552 87 E 0.0050 0.9466 0.0484 88 T 0.0047 0.9570 0.0383 89 D 0.0047 0.9571 0.0382 90 R 0.0047 0.9560 0.0393 91 L 0.0047 0.9569 0.0385 92 W 0.0047 0.9559 0.0394 93 N 0.0047 0.9546 0.0407 94 A 0.0048 0.9462 0.0490 95 I 0.0064 0.9297 0.0639 96 V 0.0091 0.8701 0.1208 97 D 0.0232 0.6320 0.3447 98 N 0.0397 0.2458 0.7146 99 G 0.0515 0.0663 0.8821 100 G 0.0926 0.0624 0.8450 101 E 0.2557 0.0863 0.6581 102 E 0.3402 0.0836 0.5762 103 S 0.3065 0.0522 0.6413 104 A 0.2805 0.0898 0.6296 105 C 0.3177 0.0779 0.6044 106 G 0.4417 0.0662 0.4921 107 W 0.6298 0.0661 0.3041 108 C 0.5922 0.0939 0.3139 109 R 0.5894 0.0967 0.3139 110 D 0.3508 0.1187 0.5305 111 K 0.1902 0.1999 0.6099 112 W 0.1879 0.1158 0.6962 113 G 0.2417 0.0760 0.6823 114 I 0.4093 0.0692 0.5215 115 S 0.4330 0.0996 0.4675 116 W 0.4930 0.1614 0.3456 117 Q 0.4958 0.1867 0.3175 118 I 0.4288 0.1750 0.3962 119 T 0.2762 0.0788 0.6450 120 P 0.0728 0.4010 0.5262 121 R 0.0074 0.8890 0.1035 122 V 0.0061 0.9172 0.0767 123 L 0.0050 0.9431 0.0519 124 S 0.0052 0.9439 0.0508 125 E 0.0056 0.9274 0.0670 126 A 0.0085 0.8800 0.1114 127 I 0.0237 0.6855 0.2907 128 A 0.0240 0.3527 0.6233 129 S 0.0689 0.0929 0.8382 130 P 0.0312 0.1221 0.8468 131 D 0.0770 0.0848 0.8382 132 R 0.0055 0.9213 0.0733 133 A 0.0057 0.9387 0.0556 134 A 0.0049 0.9436 0.0515 135 A 0.0048 0.9554 0.0399 136 R 0.0053 0.9553 0.0395 137 R 0.0050 0.9562 0.0388 138 A 0.0055 0.9559 0.0386 139 F 0.0055 0.9580 0.0365 140 E 0.0051 0.9559 0.0390 141 A 0.0052 0.9479 0.0469 142 M 0.0059 0.9174 0.0768 143 M 0.0096 0.8127 0.1777 144 T 0.0117 0.6349 0.3534 145 M 0.0351 0.4816 0.4833 146 G 0.0369 0.4894 0.4737 147 R 0.2074 0.4978 0.2949 148 I 0.2501 0.5097 0.2402 149 D 0.2490 0.5615 0.1894 150 I 0.0093 0.9392 0.0515 151 A 0.0051 0.9553 0.0396 152 T 0.0047 0.9570 0.0383 153 I 0.0047 0.9558 0.0395 154 E 0.0047 0.9483 0.0470 155 K 0.0049 0.9255 0.0696 156 A 0.0069 0.8592 0.1339 157 F 0.0165 0.7314 0.2522 158 K 0.0428 0.4193 0.5378 159 G 0.0394 0.0670 0.8936