# This file is the result of combining several RDB files, specifically # T0237.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0237.t2k.stride-ebghtl.rdb (weight 1.24869) # T0237.t2k.str2.rdb (weight 1.54758) # T0237.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 T0237.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0237 # 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 T0237.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 8 # # ============================================ # Comments from T0237.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0237 # 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 T0237.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 8 # # ============================================ # Comments from T0237.t2k.str2.rdb # ============================================ # TARGET T0237 # 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 T0237.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 8 # # ============================================ # Comments from T0237.t2k.alpha.rdb # ============================================ # TARGET T0237 # 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 T0237.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 8 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.1630 0.0515 0.7855 2 G 0.3021 0.0592 0.6387 3 L 0.5193 0.0422 0.4385 4 W 0.5342 0.0621 0.4037 5 V 0.3966 0.0591 0.5442 6 D 0.1668 0.0471 0.7861 7 G 0.1344 0.0509 0.8147 8 N 0.2169 0.1220 0.6612 9 C 0.2440 0.3071 0.4489 10 E 0.2716 0.3288 0.3997 11 E 0.2839 0.2993 0.4167 12 I 0.2756 0.1871 0.5374 13 P 0.2167 0.1342 0.6490 14 Y 0.2030 0.2055 0.5916 15 V 0.2576 0.2993 0.4431 16 K 0.3430 0.2850 0.3720 17 E 0.3536 0.2881 0.3583 18 V 0.3102 0.2717 0.4181 19 E 0.2473 0.2191 0.5336 20 A 0.0930 0.2754 0.6315 21 E 0.0592 0.1811 0.7597 22 D 0.0907 0.1250 0.7843 23 L 0.0244 0.7735 0.2022 24 R 0.0246 0.7973 0.1781 25 E 0.0415 0.7537 0.2048 26 C 0.1015 0.6671 0.2314 27 N 0.0950 0.5675 0.3375 28 R 0.2062 0.4695 0.3243 29 I 0.3899 0.3474 0.2627 30 V 0.5289 0.2195 0.2516 31 F 0.5066 0.1151 0.3783 32 G 0.2507 0.1048 0.6445 33 A 0.1273 0.1159 0.7568 34 S 0.1334 0.0678 0.7988 35 A 0.0282 0.3815 0.5903 36 S 0.0291 0.3544 0.6165 37 D 0.0498 0.2687 0.6815 38 Q 0.0902 0.1471 0.7627 39 P 0.0465 0.3551 0.5984 40 T 0.0766 0.4886 0.4348 41 Q 0.1042 0.5606 0.3352 42 Y 0.0957 0.6177 0.2866 43 E 0.0961 0.6290 0.2750 44 E 0.0576 0.6459 0.2965 45 E 0.0521 0.6286 0.3193 46 M 0.0297 0.7715 0.1987 47 T 0.0210 0.7972 0.1818 48 D 0.0136 0.8530 0.1335 49 Y 0.0062 0.9312 0.0626 50 Q 0.0057 0.9401 0.0541 51 K 0.0065 0.9379 0.0556 52 I 0.0060 0.9391 0.0548 53 Q 0.0080 0.9327 0.0594 54 Q 0.0108 0.8933 0.0959 55 G 0.0122 0.8114 0.1764 56 F 0.0219 0.7793 0.1989 57 R 0.0235 0.7733 0.2032 58 Q 0.0220 0.7003 0.2777 59 N 0.0314 0.5368 0.4318 60 N 0.0522 0.3315 0.6163 61 R 0.0101 0.7902 0.1998 62 E 0.0099 0.8190 0.1711 63 M 0.0132 0.8527 0.1341 64 I 0.0156 0.8636 0.1208 65 K 0.0239 0.8192 0.1569 66 S 0.0347 0.7874 0.1779 67 A 0.0606 0.6780 0.2613 68 F 0.1897 0.3996 0.4107 69 L 0.2070 0.1770 0.6159 70 P 0.1951 0.1724 0.6325 71 V 0.2029 0.2022 0.5949 72 G 0.2341 0.1696 0.5963 73 A 0.3541 0.1403 0.5055 74 F 0.4727 0.1055 0.4218 75 N 0.4461 0.0864 0.4676 76 S 0.3024 0.1102 0.5874 77 D 0.1467 0.1042 0.7491 78 N 0.2368 0.0929 0.6703 79 F 0.5669 0.0554 0.3777 80 K 0.6262 0.0572 0.3167 81 S 0.5394 0.0526 0.4080 82 K 0.2887 0.0707 0.6406 83 G 0.2313 0.0709 0.6978 84 R 0.3103 0.0606 0.6291 85 G 0.3739 0.0525 0.5736 86 F 0.4792 0.0481 0.4727 87 N 0.4704 0.0624 0.4672 88 W 0.4128 0.1360 0.4512 89 A 0.4696 0.1271 0.4033 90 N 0.4765 0.1007 0.4228 91 F 0.4832 0.0552 0.4615 92 D 0.2771 0.0596 0.6634 93 S 0.0404 0.1884 0.7712 94 V 0.0366 0.1634 0.8000 95 K 0.0704 0.0683 0.8613 96 K 0.1045 0.0466 0.8489 97 K 0.5978 0.0221 0.3802 98 C 0.8158 0.0140 0.1702 99 Y 0.8395 0.0139 0.1466 100 I 0.8487 0.0196 0.1317 101 F 0.7658 0.0306 0.2036 102 N 0.5267 0.0241 0.4492 103 T 0.2136 0.0352 0.7513 104 K 0.1272 0.0202 0.8525 105 P 0.1433 0.0735 0.7833 106 T 0.3468 0.0794 0.5738 107 C 0.6039 0.0691 0.3270 108 L 0.7068 0.0620 0.2312 109 I 0.7192 0.0517 0.2292 110 N 0.5764 0.0440 0.3797 111 D 0.2760 0.0413 0.6827 112 K 0.0362 0.1702 0.7935 113 N 0.0342 0.2412 0.7245 114 F 0.3089 0.3220 0.3691 115 I 0.4749 0.3501 0.1750 116 A 0.5258 0.3364 0.1378 117 T 0.4694 0.3767 0.1539 118 T 0.3524 0.4271 0.2205 119 A 0.2783 0.4596 0.2621 120 L 0.2016 0.3898 0.4086 121 S 0.1026 0.2438 0.6535 122 H 0.0914 0.1024 0.8062 123 P 0.0675 0.2128 0.7197 124 Q 0.0449 0.1838 0.7712 125 E 0.0374 0.1726 0.7899