# This file is the result of combining several RDB files, specifically # T0312.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0312.t2k.stride-ebghtl.rdb (weight 1.24869) # T0312.t2k.str2.rdb (weight 1.54758) # T0312.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 T0312.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0312 # 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 T0312.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 78 # # ============================================ # Comments from T0312.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0312 # 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 T0312.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 78 # # ============================================ # Comments from T0312.t2k.str2.rdb # ============================================ # TARGET T0312 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0312.t2k-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 69.939 # # ============================================ # Comments from T0312.t2k.alpha.rdb # ============================================ # TARGET T0312 # 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 T0312.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 78 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0960 0.0525 0.8515 2 K 0.2442 0.0764 0.6794 3 V 0.3364 0.0961 0.5675 4 F 0.4673 0.1070 0.4257 5 E 0.5832 0.0885 0.3283 6 F 0.4071 0.0889 0.5039 7 E 0.3056 0.0675 0.6269 8 V 0.2013 0.0738 0.7248 9 G 0.1487 0.0454 0.8058 10 K 0.3808 0.0206 0.5986 11 G 0.8359 0.0039 0.1602 12 F 0.9140 0.0034 0.0826 13 L 0.9261 0.0035 0.0704 14 L 0.9153 0.0044 0.0803 15 R 0.8886 0.0044 0.1070 16 L 0.5590 0.0106 0.4304 17 D 0.1242 0.0233 0.8524 18 Y 0.0238 0.0761 0.9000 19 G 0.0210 0.0783 0.9007 20 K 0.0727 0.4196 0.5077 21 D 0.0769 0.7175 0.2056 22 L 0.0112 0.9265 0.0623 23 V 0.0055 0.9526 0.0418 24 R 0.0052 0.9542 0.0406 25 Q 0.0047 0.9580 0.0373 26 I 0.0047 0.9589 0.0364 27 E 0.0047 0.9597 0.0356 28 E 0.0047 0.9580 0.0373 29 F 0.0047 0.9569 0.0384 30 L 0.0048 0.9490 0.0462 31 E 0.0051 0.9250 0.0699 32 E 0.0094 0.8205 0.1701 33 K 0.0416 0.4291 0.5292 34 G 0.0471 0.0468 0.9060 35 I 0.1048 0.0181 0.8771 36 H 0.2396 0.0561 0.7043 37 A 0.7605 0.0281 0.2114 38 A 0.8377 0.0206 0.1417 39 H 0.9041 0.0126 0.0833 40 I 0.9152 0.0099 0.0750 41 S 0.8671 0.0270 0.1060 42 A 0.7408 0.0677 0.1915 43 I 0.5860 0.1616 0.2524 44 G 0.4691 0.2085 0.3225 45 A 0.4101 0.2700 0.3199 46 V 0.3785 0.2842 0.3373 47 R 0.2739 0.2945 0.4316 48 S 0.3154 0.2318 0.4528 49 A 0.4826 0.1475 0.3699 50 V 0.6870 0.0977 0.2153 51 I 0.7578 0.0689 0.1733 52 G 0.7530 0.0508 0.1962 53 Y 0.7270 0.0346 0.2384 54 Y 0.4805 0.0377 0.4818 55 D 0.2265 0.0317 0.7417 56 Q 0.0500 0.3268 0.6232 57 E 0.0598 0.3317 0.6085 58 K 0.0916 0.3501 0.5582 59 K 0.1447 0.2346 0.6207 60 E 0.2593 0.1715 0.5692 61 Y 0.3268 0.1050 0.5682 62 V 0.3982 0.0696 0.5322 63 K 0.4415 0.0578 0.5007 64 K 0.4586 0.0517 0.4897 65 E 0.4920 0.0358 0.4722 66 L 0.3295 0.0640 0.6065 67 M 0.1514 0.0777 0.7709 68 E 0.1443 0.0475 0.8081 69 P 0.3027 0.0875 0.6098 70 L 0.6326 0.0577 0.3097 71 E 0.8465 0.0341 0.1194 72 I 0.8655 0.0382 0.0963 73 L 0.8271 0.0439 0.1290 74 S 0.8326 0.0339 0.1334 75 L 0.7914 0.0338 0.1748 76 S 0.7173 0.0381 0.2447 77 G 0.6511 0.0274 0.3215 78 N 0.6984 0.0162 0.2854 79 V 0.6550 0.0167 0.3283 80 S 0.5541 0.0250 0.4209 81 M 0.1516 0.1418 0.7066 82 K 0.0471 0.1316 0.8213 83 D 0.0533 0.0422 0.9045 84 S 0.0438 0.0371 0.9191 85 K 0.2446 0.0119 0.7435 86 P 0.6031 0.0059 0.3910 87 F 0.7537 0.0109 0.2354 88 C 0.8939 0.0044 0.1017 89 H 0.9046 0.0063 0.0892 90 I 0.9144 0.0046 0.0810 91 H 0.9126 0.0047 0.0827 92 V 0.8933 0.0073 0.0994 93 L 0.8614 0.0078 0.1308 94 L 0.7523 0.0131 0.2346 95 G 0.3044 0.0210 0.6746 96 K 0.0495 0.0923 0.8582 97 D 0.0514 0.0309 0.9178 98 G 0.0735 0.0351 0.8914 99 E 0.4258 0.0205 0.5537 100 V 0.7451 0.0122 0.2426 101 Y 0.6931 0.0314 0.2755 102 G 0.6163 0.0417 0.3420 103 G 0.4848 0.0725 0.4427 104 H 0.5598 0.0713 0.3689 105 L 0.4927 0.0987 0.4086 106 F 0.2828 0.1388 0.5784 107 S 0.1574 0.1440 0.6986 108 A 0.2307 0.0780 0.6913 109 E 0.5459 0.0284 0.4257 110 V 0.7192 0.0179 0.2630 111 F 0.7596 0.0161 0.2243 112 A 0.7999 0.0204 0.1797 113 C 0.8420 0.0151 0.1428 114 E 0.8977 0.0102 0.0921 115 V 0.9209 0.0052 0.0739 116 F 0.9176 0.0073 0.0751 117 V 0.9167 0.0064 0.0769 118 L 0.8750 0.0176 0.1074 119 P 0.8201 0.0216 0.1583 120 L 0.5782 0.0448 0.3770 121 S 0.2008 0.0676 0.7316 122 G 0.0814 0.0917 0.8268 123 E 0.1875 0.1141 0.6983 124 A 0.2901 0.1413 0.5687 125 P 0.3673 0.2126 0.4201 126 E 0.4282 0.2250 0.3468 127 R 0.5127 0.1778 0.3095 128 A 0.5500 0.1247 0.3253 129 F 0.4681 0.0830 0.4490 130 D 0.1794 0.0479 0.7727 131 E 0.0115 0.3542 0.6343 132 Q 0.0163 0.2861 0.6975 133 T 0.0742 0.2277 0.6981 134 G 0.0949 0.0932 0.8119 135 L 0.2281 0.1844 0.5876 136 F 0.2959 0.2247 0.4794 137 L 0.3022 0.2903 0.4075 138 W 0.3285 0.1697 0.5019 139 L 0.2683 0.1327 0.5990 140 E 0.2409 0.3081 0.4510 141 H 0.1740 0.3686 0.4573 142 H 0.2559 0.3102 0.4339 143 H 0.2361 0.2457 0.5181 144 H 0.1862 0.1796 0.6342 145 H 0.1158 0.1169 0.7673 146 H 0.0604 0.0463 0.8934