# This file is the result of combining several RDB files, specifically # T0196.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0196.t2k.stride-ebghtl.rdb (weight 1.24869) # T0196.t2k.str2.rdb (weight 1.54758) # T0196.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 T0196.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0196 # 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 T0196.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 545 # # ============================================ # Comments from T0196.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0196 # 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 T0196.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 545 # # ============================================ # Comments from T0196.t2k.str2.rdb # ============================================ # TARGET T0196 # 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 T0196.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 545 # # ============================================ # Comments from T0196.t2k.alpha.rdb # ============================================ # TARGET T0196 # 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 T0196.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 545 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0425 0.1479 0.8096 2 H 0.0551 0.1830 0.7619 3 H 0.0502 0.2348 0.7150 4 H 0.0489 0.3440 0.6071 5 H 0.0456 0.5310 0.4235 6 H 0.0445 0.5726 0.3829 7 H 0.0463 0.5447 0.4090 8 G 0.0195 0.7340 0.2465 9 S 0.0072 0.9138 0.0790 10 G 0.0062 0.9327 0.0611 11 L 0.0048 0.9485 0.0466 12 F 0.0048 0.9489 0.0464 13 D 0.0051 0.9418 0.0531 14 F 0.0051 0.9239 0.0709 15 L 0.0114 0.8945 0.0942 16 K 0.0081 0.8265 0.1654 17 R 0.0147 0.6241 0.3612 18 K 0.0721 0.3358 0.5920 19 E 0.0928 0.1290 0.7781 20 V 0.0796 0.0951 0.8253 21 K 0.0832 0.1259 0.7909 22 E 0.0838 0.1310 0.7852 23 E 0.0710 0.1710 0.7581 24 E 0.0703 0.2095 0.7202 25 K 0.0856 0.3515 0.5628 26 I 0.0867 0.3600 0.5533 27 E 0.1155 0.2737 0.6108 28 I 0.0948 0.2537 0.6514 29 L 0.1025 0.1881 0.7095 30 S 0.0678 0.0784 0.8538 31 K 0.0718 0.0973 0.8309 32 K 0.0600 0.0749 0.8651 33 P 0.0698 0.0561 0.8741 34 A 0.1353 0.0841 0.7806 35 G 0.2948 0.0546 0.6506 36 K 0.5498 0.0431 0.4070 37 V 0.5476 0.0179 0.4345 38 V 0.4637 0.0222 0.5141 39 V 0.3015 0.3324 0.3661 40 E 0.1807 0.4403 0.3789 41 E 0.2958 0.3601 0.3441 42 V 0.5485 0.1009 0.3506 43 V 0.7390 0.0411 0.2198 44 N 0.7632 0.0254 0.2114 45 I 0.5615 0.0420 0.3965 46 M 0.2116 0.0411 0.7473 47 G 0.1735 0.0386 0.7879 48 K 0.4966 0.0268 0.4766 49 D 0.7368 0.0108 0.2523 50 V 0.8385 0.0072 0.1543 51 I 0.8297 0.0059 0.1644 52 I 0.7172 0.0246 0.2582 53 G 0.7669 0.0122 0.2209 54 T 0.8459 0.0100 0.1441 55 V 0.8332 0.0136 0.1531 56 E 0.7612 0.0337 0.2051 57 S 0.5329 0.0380 0.4291 58 G 0.4307 0.0283 0.5409 59 M 0.6595 0.0117 0.3288 60 I 0.7273 0.0069 0.2657 61 G 0.3031 0.0134 0.6835 62 V 0.0570 0.0624 0.8806 63 G 0.0283 0.0405 0.9312 64 F 0.2793 0.0124 0.7083 65 K 0.8018 0.0032 0.1950 66 V 0.9112 0.0040 0.0848 67 K 0.9177 0.0037 0.0785 68 G 0.8806 0.0052 0.1143 69 P 0.6478 0.0144 0.3379 70 S 0.2896 0.0214 0.6890 71 G 0.2474 0.0280 0.7246 72 I 0.3959 0.0294 0.5748 73 G 0.5551 0.0134 0.4316 74 G 0.7950 0.0095 0.1955 75 I 0.8487 0.0102 0.1411 76 V 0.7632 0.0437 0.1931 77 R 0.7630 0.0228 0.2142 78 I 0.7520 0.0469 0.2011 79 E 0.7416 0.0569 0.2015 80 R 0.5943 0.0811 0.3245 81 N 0.3481 0.0970 0.5549 82 R 0.2209 0.1318 0.6474 83 E 0.1820 0.1913 0.6267 84 K 0.2332 0.2463 0.5205 85 V 0.1105 0.4704 0.4192 86 E 0.0873 0.4666 0.4461 87 F 0.1633 0.3816 0.4551 88 A 0.2399 0.1247 0.6354 89 I 0.2220 0.0532 0.7248 90 A 0.1308 0.1549 0.7143 91 G 0.0858 0.1380 0.7762 92 D 0.1449 0.1191 0.7360 93 R 0.4780 0.0338 0.4882 94 I 0.6646 0.0215 0.3139 95 G 0.8274 0.0143 0.1583 96 I 0.8747 0.0098 0.1155 97 S 0.8704 0.0089 0.1207 98 I 0.7942 0.0196 0.1862 99 E 0.4727 0.0549 0.4723 100 G 0.2786 0.0304 0.6910 101 K 0.2888 0.0275 0.6837 102 I 0.2711 0.0889 0.6400 103 G 0.2489 0.1755 0.5756 104 K 0.3753 0.2048 0.4199 105 V 0.4185 0.1940 0.3875 106 K 0.5051 0.1667 0.3282 107 K 0.3272 0.1554 0.5174 108 G 0.2167 0.0590 0.7243 109 D 0.4030 0.0397 0.5573 110 V 0.7082 0.0249 0.2670 111 L 0.5952 0.0494 0.3554 112 E 0.4767 0.0306 0.4926 113 I 0.2039 0.0332 0.7629 114 Y 0.0682 0.0921 0.8397 115 Q 0.0547 0.0609 0.8844 116 T 0.0567 0.0253 0.9181