# This file is the result of combining several RDB files, specifically # T0406.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0406.t2k.stride-ebghtl.rdb (weight 1.24869) # T0406.t2k.str2.rdb (weight 1.54758) # T0406.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 T0406.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0406 # 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 T0406.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 180 # # ============================================ # Comments from T0406.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0406 # 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 T0406.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 180 # # ============================================ # Comments from T0406.t2k.str2.rdb # ============================================ # TARGET T0406 # 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 T0406.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 180 # # ============================================ # Comments from T0406.t2k.alpha.rdb # ============================================ # TARGET T0406 # 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 T0406.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 180 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0172 0.4167 0.5661 2 Y 0.0137 0.8019 0.1844 3 Q 0.0110 0.8783 0.1107 4 T 0.0070 0.9105 0.0825 5 I 0.0050 0.9482 0.0468 6 E 0.0050 0.9545 0.0405 7 G 0.0048 0.9554 0.0398 8 F 0.0048 0.9535 0.0417 9 L 0.0049 0.9504 0.0447 10 Q 0.0049 0.9401 0.0550 11 S 0.0062 0.9158 0.0780 12 W 0.0080 0.9059 0.0861 13 T 0.0054 0.9145 0.0801 14 Y 0.0053 0.9066 0.0881 15 E 0.0062 0.9049 0.0889 16 T 0.0068 0.9128 0.0804 17 E 0.0058 0.9257 0.0685 18 S 0.0054 0.9399 0.0547 19 T 0.0048 0.9485 0.0467 20 Q 0.0047 0.9552 0.0400 21 K 0.0047 0.9551 0.0401 22 M 0.0048 0.9522 0.0431 23 L 0.0050 0.9304 0.0647 24 D 0.0057 0.8276 0.1666 25 V 0.0124 0.5252 0.4624 26 L 0.0540 0.0881 0.8579 27 T 0.0533 0.0388 0.9079 28 D 0.0092 0.7149 0.2759 29 E 0.0110 0.7429 0.2461 30 S 0.0133 0.8154 0.1713 31 L 0.0370 0.6808 0.2822 32 S 0.0545 0.5281 0.4174 33 Q 0.0671 0.4077 0.5253 34 E 0.0940 0.1782 0.7279 35 I 0.0828 0.1893 0.7279 36 A 0.0640 0.2039 0.7321 37 P 0.0260 0.2823 0.6917 38 G 0.0303 0.2260 0.7436 39 H 0.0683 0.1995 0.7322 40 W 0.0693 0.1935 0.7372 41 T 0.0880 0.2349 0.6772 42 L 0.0050 0.9437 0.0512 43 G 0.0047 0.9565 0.0388 44 R 0.0047 0.9567 0.0386 45 V 0.0047 0.9592 0.0361 46 A 0.0047 0.9588 0.0365 47 W 0.0047 0.9565 0.0388 48 H 0.0047 0.9534 0.0418 49 I 0.0048 0.9528 0.0424 50 V 0.0051 0.9402 0.0547 51 T 0.0054 0.9226 0.0721 52 A 0.0067 0.9205 0.0728 53 I 0.0056 0.9399 0.0546 54 P 0.0052 0.9496 0.0452 55 V 0.0054 0.9494 0.0452 56 I 0.0067 0.9442 0.0491 57 L 0.0073 0.9312 0.0615 58 S 0.0093 0.8903 0.1004 59 G 0.0144 0.8337 0.1518 60 T 0.0434 0.6952 0.2613 61 G 0.0507 0.4447 0.5046 62 L 0.0527 0.2093 0.7380 63 K 0.0689 0.1314 0.7997 64 F 0.0931 0.1296 0.7773 65 E 0.0929 0.1357 0.7714 66 G 0.0890 0.1288 0.7822 67 E 0.0892 0.1931 0.7177 68 T 0.0891 0.1920 0.7189 69 K 0.0943 0.1939 0.7118 70 D 0.0868 0.1804 0.7328 71 Y 0.0795 0.1429 0.7777 72 P 0.0795 0.1735 0.7471 73 V 0.0870 0.1455 0.7675 74 P 0.0874 0.1748 0.7378 75 T 0.0754 0.3125 0.6121 76 S 0.0384 0.4190 0.5426 77 A 0.0486 0.4829 0.4685 78 K 0.0057 0.9032 0.0911 79 T 0.0058 0.9328 0.0615 80 I 0.0051 0.9427 0.0522 81 A 0.0048 0.9481 0.0470 82 D 0.0048 0.9512 0.0440 83 G 0.0050 0.9430 0.0521 84 Y 0.0053 0.9329 0.0617 85 R 0.0060 0.9266 0.0674 86 K 0.0057 0.9171 0.0772 87 V 0.0064 0.9017 0.0919 88 N 0.0068 0.8905 0.1027 89 T 0.0056 0.9152 0.0791 90 A 0.0052 0.9345 0.0603 91 F 0.0052 0.9416 0.0532 92 V 0.0051 0.9486 0.0463 93 E 0.0048 0.9521 0.0432 94 A 0.0049 0.9481 0.0470 95 L 0.0051 0.9368 0.0581 96 Q 0.0061 0.8913 0.1026 97 S 0.0093 0.6841 0.3066 98 E 0.0169 0.3649 0.6182 99 W 0.0670 0.0717 0.8613 100 T 0.0549 0.0305 0.9147 101 D 0.0083 0.8214 0.1703 102 K 0.0088 0.8536 0.1375 103 D 0.0122 0.8761 0.1116 104 L 0.0378 0.8145 0.1477 105 T 0.0651 0.7211 0.2138 106 T 0.0699 0.6486 0.2815 107 I 0.1365 0.4420 0.4214 108 N 0.1876 0.2616 0.5508 109 D 0.1639 0.1934 0.6428 110 F 0.1149 0.1830 0.7021 111 F 0.0963 0.1605 0.7432 112 G 0.0991 0.1098 0.7911 113 R 0.1525 0.0781 0.7694 114 P 0.1739 0.0650 0.7612 115 M 0.1219 0.0720 0.8061 116 P 0.0907 0.1011 0.8082 117 N 0.0056 0.9287 0.0657 118 S 0.0047 0.9518 0.0434 119 I 0.0047 0.9580 0.0373 120 F 0.0047 0.9606 0.0347 121 L 0.0050 0.9597 0.0353 122 M 0.0047 0.9600 0.0353 123 T 0.0047 0.9587 0.0366 124 L 0.0050 0.9555 0.0395 125 I 0.0049 0.9459 0.0492 126 N 0.0057 0.9078 0.0864 127 H 0.0083 0.8335 0.1582 128 Q 0.0097 0.8172 0.1731 129 N 0.0101 0.8422 0.1477 130 H 0.0209 0.7658 0.2133 131 H 0.0345 0.7616 0.2039 132 R 0.0104 0.8540 0.1356 133 G 0.0097 0.8794 0.1109 134 Q 0.0057 0.9508 0.0435 135 M 0.0047 0.9601 0.0352 136 T 0.0050 0.9599 0.0351 137 V 0.0050 0.9607 0.0343 138 L 0.0053 0.9598 0.0349 139 M 0.0050 0.9577 0.0372 140 R 0.0052 0.9453 0.0495 141 Q 0.0066 0.9090 0.0845 142 A 0.0437 0.5019 0.4543 143 G 0.0374 0.0383 0.9244 144 L 0.0731 0.0146 0.9123 145 T 0.1380 0.0166 0.8454 146 V 0.1337 0.0286 0.8376 147 P 0.1322 0.0605 0.8073 148 G 0.1772 0.1084 0.7144 149 V 0.1788 0.1213 0.6999 150 Y 0.1325 0.0917 0.7759 151 G 0.1100 0.0512 0.8387 152 P 0.0917 0.0834 0.8249 153 A 0.0801 0.1289 0.7910 154 K 0.0340 0.5361 0.4298 155 E 0.0128 0.7528 0.2344 156 E 0.0101 0.7914 0.1985 157 W 0.0144 0.7961 0.1895 158 A 0.0188 0.8005 0.1807 159 T 0.0233 0.7949 0.1818 160 A 0.0513 0.6099 0.3388 161 G 0.0445 0.3198 0.6357 162 M 0.0580 0.3180 0.6240 163 E 0.0777 0.2890 0.6333 164 A 0.0793 0.1298 0.7909 165 P 0.0757 0.0882 0.8360 166 K 0.1048 0.0701 0.8251 167 M 0.0546 0.0273 0.9181