# This file is the result of combining several RDB files, specifically # T0229.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0229.t2k.stride-ebghtl.rdb (weight 1.24869) # T0229.t2k.str2.rdb (weight 1.54758) # T0229.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 T0229.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0229 # 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 T0229.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 112 # # ============================================ # Comments from T0229.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0229 # 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 T0229.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 112 # # ============================================ # Comments from T0229.t2k.str2.rdb # ============================================ # TARGET T0229 # 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 T0229.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 112 # # ============================================ # Comments from T0229.t2k.alpha.rdb # ============================================ # TARGET T0229 # 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 T0229.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 112 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1667 0.0142 0.8191 2 Q 0.6384 0.0106 0.3510 3 A 0.8060 0.0066 0.1874 4 R 0.8562 0.0070 0.1368 5 W 0.7838 0.0087 0.2075 6 I 0.4596 0.0401 0.5003 7 G 0.0887 0.0504 0.8610 8 N 0.0673 0.0541 0.8785 9 M 0.5096 0.0205 0.4698 10 M 0.8420 0.0080 0.1500 11 F 0.9022 0.0046 0.0931 12 H 0.9147 0.0046 0.0808 13 V 0.8998 0.0047 0.0955 14 R 0.8812 0.0066 0.1121 15 T 0.7031 0.0146 0.2823 16 D 0.2210 0.0581 0.7209 17 S 0.0914 0.0487 0.8598 18 N 0.1640 0.0591 0.7769 19 H 0.5813 0.0215 0.3971 20 D 0.8616 0.0058 0.1327 21 V 0.8920 0.0048 0.1032 22 L 0.8588 0.0072 0.1340 23 M 0.7328 0.0130 0.2542 24 D 0.4292 0.0313 0.5396 25 T 0.2238 0.0430 0.7332 26 K 0.1643 0.0728 0.7629 27 E 0.0875 0.3153 0.5972 28 E 0.0638 0.3512 0.5850 29 V 0.0614 0.2720 0.6666 30 G 0.0569 0.1116 0.8316 31 G 0.0726 0.0974 0.8300 32 K 0.0788 0.1318 0.7894 33 D 0.0724 0.1246 0.8030 34 A 0.0649 0.0932 0.8420 35 A 0.0750 0.0481 0.8769 36 P 0.0994 0.0515 0.8491 37 R 0.0811 0.0534 0.8655 38 P 0.0083 0.9040 0.0878 39 L 0.0049 0.9493 0.0459 40 E 0.0048 0.9567 0.0385 41 L 0.0047 0.9580 0.0373 42 V 0.0048 0.9561 0.0391 43 L 0.0048 0.9540 0.0412 44 T 0.0050 0.9496 0.0454 45 G 0.0051 0.9373 0.0576 46 L 0.0061 0.9137 0.0802 47 M 0.0068 0.8696 0.1236 48 G 0.0077 0.8436 0.1487 49 C 0.0096 0.8512 0.1392 50 T 0.0080 0.8824 0.1097 51 G 0.0071 0.9213 0.0715 52 M 0.0064 0.9409 0.0527 53 D 0.0058 0.9515 0.0428 54 V 0.0047 0.9580 0.0373 55 V 0.0047 0.9597 0.0356 56 S 0.0047 0.9590 0.0363 57 I 0.0047 0.9573 0.0380 58 L 0.0048 0.9466 0.0486 59 R 0.0054 0.8999 0.0947 60 K 0.0100 0.7774 0.2126 61 M 0.0473 0.3579 0.5949 62 K 0.0400 0.1050 0.8550 63 V 0.0959 0.1131 0.7910 64 I 0.1614 0.0789 0.7597 65 D 0.1057 0.0388 0.8555 66 Q 0.2589 0.0488 0.6923 67 M 0.2061 0.1522 0.6417 68 K 0.1427 0.1773 0.6800 69 D 0.2229 0.1321 0.6449 70 F 0.5487 0.0158 0.4355 71 R 0.7933 0.0051 0.2016 72 I 0.8905 0.0040 0.1055 73 E 0.9027 0.0038 0.0935 74 I 0.8820 0.0044 0.1136 75 E 0.8651 0.0061 0.1289 76 Y 0.7722 0.0116 0.2161 77 E 0.6481 0.0178 0.3341 78 R 0.4258 0.0328 0.5414 79 T 0.1749 0.0413 0.7838 80 E 0.0568 0.1457 0.7975 81 E 0.0597 0.1112 0.8291 82 H 0.0909 0.0735 0.8356 83 P 0.1472 0.0806 0.7722 84 R 0.3689 0.0664 0.5647 85 I 0.5658 0.0489 0.3854 86 F 0.6479 0.0244 0.3277 87 T 0.7165 0.0191 0.2644 88 K 0.8457 0.0066 0.1477 89 V 0.8821 0.0036 0.1142 90 H 0.9147 0.0033 0.0820 91 L 0.9265 0.0032 0.0703 92 K 0.9291 0.0031 0.0677 93 Y 0.9267 0.0034 0.0699 94 I 0.9194 0.0033 0.0773 95 F 0.8852 0.0043 0.1105 96 K 0.6403 0.0142 0.3455 97 F 0.2216 0.0215 0.7568 98 D 0.0539 0.0528 0.8932 99 G 0.0329 0.0489 0.9182 100 E 0.0533 0.0392 0.9075 101 P 0.1161 0.0231 0.8608 102 P 0.0795 0.0178 0.9026 103 K 0.0052 0.9037 0.0911 104 D 0.0048 0.9172 0.0780 105 K 0.0050 0.9427 0.0523 106 V 0.0047 0.9574 0.0379 107 E 0.0047 0.9573 0.0379 108 K 0.0047 0.9558 0.0395 109 A 0.0047 0.9550 0.0403 110 V 0.0047 0.9544 0.0409 111 Q 0.0049 0.9415 0.0536 112 L 0.0052 0.9300 0.0648 113 S 0.0060 0.8941 0.0999 114 Q 0.0062 0.8287 0.1651 115 E 0.0086 0.7519 0.2394 116 K 0.0166 0.4660 0.5174 117 Y 0.0389 0.3930 0.5681 118 C 0.0524 0.2406 0.7070 119 S 0.0722 0.5355 0.3923 120 V 0.0561 0.7899 0.1541 121 S 0.0571 0.8245 0.1184 122 A 0.0453 0.8295 0.1252 123 I 0.0503 0.7862 0.1635 124 L 0.1002 0.6046 0.2952 125 K 0.0971 0.3267 0.5762 126 C 0.0594 0.1314 0.8093 127 S 0.0933 0.0560 0.8507 128 S 0.2680 0.0108 0.7212 129 K 0.5517 0.0040 0.4443 130 V 0.8383 0.0036 0.1580 131 T 0.8768 0.0035 0.1197 132 Y 0.8904 0.0042 0.1054 133 E 0.9095 0.0033 0.0872 134 I 0.9004 0.0038 0.0958 135 V 0.8922 0.0034 0.1044 136 Y 0.7616 0.0100 0.2284 137 E 0.3678 0.0329 0.5993 138 N 0.0967 0.0310 0.8723