# This file is the result of combining several RDB files, specifically # T0383.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0383.t2k.stride-ebghtl.rdb (weight 1.24869) # T0383.t2k.str2.rdb (weight 1.54758) # T0383.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 T0383.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0383 # 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 T0383.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 17 # # ============================================ # Comments from T0383.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0383 # 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 T0383.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 17 # # ============================================ # Comments from T0383.t2k.str2.rdb # ============================================ # TARGET T0383 # 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 T0383.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 17 # # ============================================ # Comments from T0383.t2k.alpha.rdb # ============================================ # TARGET T0383 # 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 T0383.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 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0773 0.0697 0.8531 2 N 0.1587 0.0899 0.7514 3 A 0.2140 0.1768 0.6092 4 M 0.3062 0.1922 0.5016 5 N 0.5088 0.1096 0.3816 6 L 0.5735 0.1143 0.3122 7 K 0.5752 0.0824 0.3423 8 R 0.5057 0.0858 0.4086 9 E 0.3731 0.0441 0.5828 10 Q 0.4219 0.1242 0.4540 11 E 0.6077 0.1325 0.2597 12 F 0.7710 0.0806 0.1484 13 V 0.6852 0.0856 0.2292 14 S 0.5604 0.1179 0.3217 15 Q 0.5222 0.1629 0.3149 16 Y 0.4830 0.1491 0.3678 17 H 0.4784 0.1283 0.3933 18 F 0.3261 0.2241 0.4498 19 D 0.3381 0.2129 0.4489 20 A 0.2973 0.2394 0.4633 21 R 0.2624 0.1790 0.5586 22 N 0.1516 0.1108 0.7376 23 F 0.0563 0.3432 0.6005 24 E 0.0567 0.3718 0.5716 25 W 0.0901 0.3696 0.5403 26 E 0.1266 0.3888 0.4847 27 N 0.1743 0.3724 0.4533 28 E 0.1639 0.3018 0.5343 29 N 0.1162 0.1261 0.7576 30 G 0.0870 0.0356 0.8774 31 A 0.1473 0.0221 0.8306 32 P 0.2623 0.0192 0.7185 33 E 0.5039 0.0266 0.4695 34 T 0.6988 0.0242 0.2770 35 K 0.7731 0.0149 0.2121 36 V 0.7615 0.0120 0.2266 37 D 0.8098 0.0072 0.1829 38 V 0.7588 0.0109 0.2303 39 N 0.6284 0.0176 0.3541 40 F 0.4161 0.1193 0.4646 41 Q 0.2852 0.1661 0.5487 42 L 0.2259 0.1899 0.5842 43 L 0.1484 0.2049 0.6468 44 Q 0.1319 0.2048 0.6633 45 H 0.0556 0.5852 0.3592 46 D 0.0509 0.6102 0.3390 47 Q 0.0464 0.6260 0.3276 48 E 0.0572 0.4872 0.4556 49 N 0.0509 0.2368 0.7123 50 Q 0.0838 0.0643 0.8519 51 V 0.3026 0.0168 0.6806 52 T 0.6233 0.0126 0.3641 53 S 0.8703 0.0039 0.1259 54 L 0.9189 0.0032 0.0780 55 I 0.9237 0.0035 0.0729 56 V 0.9188 0.0037 0.0775 57 I 0.9148 0.0041 0.0811 58 L 0.8856 0.0051 0.1093 59 S 0.8559 0.0059 0.1382 60 F 0.8468 0.0063 0.1469 61 M 0.8645 0.0057 0.1298 62 I 0.8526 0.0094 0.1379 63 V 0.6479 0.0253 0.3268 64 F 0.2290 0.0687 0.7023 65 D 0.0788 0.1081 0.8131 66 K 0.3276 0.0692 0.6032 67 F 0.7853 0.0196 0.1951 68 V 0.8585 0.0155 0.1260 69 I 0.8309 0.0312 0.1379 70 S 0.7261 0.0590 0.2149 71 G 0.5798 0.0908 0.3294 72 T 0.6242 0.1748 0.2010 73 I 0.5595 0.2782 0.1623 74 S 0.4560 0.3514 0.1925 75 Q 0.4637 0.3936 0.1426 76 V 0.4456 0.4252 0.1292 77 N 0.3972 0.4607 0.1421 78 H 0.4018 0.4517 0.1465 79 I 0.3235 0.4939 0.1826 80 D 0.1866 0.4337 0.3796 81 G 0.0825 0.3588 0.5588 82 R 0.1071 0.3387 0.5542 83 I 0.2209 0.2860 0.4931 84 V 0.0907 0.1717 0.7376 85 N 0.0481 0.0864 0.8655 86 E 0.0677 0.0500 0.8822 87 P 0.0308 0.4237 0.5455 88 S 0.0208 0.4578 0.5213 89 E 0.0415 0.4499 0.5086 90 L 0.0822 0.1900 0.7278 91 N 0.0558 0.1229 0.8213 92 Q 0.0063 0.9061 0.0876 93 E 0.0056 0.9313 0.0631 94 E 0.0055 0.9353 0.0592 95 V 0.0053 0.9401 0.0545 96 E 0.0050 0.9327 0.0623 97 T 0.0055 0.9121 0.0824 98 L 0.0070 0.8711 0.1219 99 A 0.0089 0.8349 0.1563 100 R 0.0089 0.8343 0.1567 101 P 0.0061 0.8640 0.1299 102 C 0.0055 0.9311 0.0633 103 L 0.0047 0.9522 0.0431 104 N 0.0048 0.9465 0.0487 105 M 0.0054 0.9367 0.0579 106 L 0.0052 0.9426 0.0522 107 N 0.0080 0.9225 0.0694 108 R 0.0067 0.8869 0.1064 109 L 0.0171 0.7769 0.2060 110 T 0.0353 0.7169 0.2478 111 Y 0.0724 0.7075 0.2201 112 E 0.1645 0.6881 0.1474 113 V 0.2201 0.6636 0.1163 114 T 0.2744 0.5898 0.1358 115 E 0.2679 0.5973 0.1348 116 I 0.2299 0.6167 0.1534 117 A 0.2490 0.5394 0.2116 118 L 0.2220 0.3801 0.3979 119 D 0.1000 0.1829 0.7171 120 L 0.0844 0.0947 0.8210 121 P 0.0505 0.0908 0.8587 122 G 0.0892 0.0800 0.8308 123 I 0.3096 0.0404 0.6500 124 N 0.4417 0.0420 0.5163 125 L 0.3596 0.1180 0.5224 126 E 0.2252 0.0905 0.6843 127 F 0.0609 0.0328 0.9063