# This file is the result of combining several RDB files, specifically # T0206.t04.dssp-ebghstl.rdb (weight 1.53986) # T0206.t04.stride-ebghtl.rdb (weight 1.24869) # T0206.t04.str2.rdb (weight 1.54758) # T0206.t04.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 T0206.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0206 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0206.t04-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 1.91129 # # ============================================ # Comments from T0206.t04.stride-ebghtl.rdb # ============================================ # TARGET T0206 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0206.t04-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 1.91129 # # ============================================ # Comments from T0206.t04.str2.rdb # ============================================ # TARGET T0206 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0206.t04-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 1.91129 # # ============================================ # Comments from T0206.t04.alpha.rdb # ============================================ # TARGET T0206 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0206.t04-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 1.91129 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0910 0.1490 0.7600 2 G 0.0778 0.0693 0.8529 3 L 0.0994 0.0458 0.8548 4 P 0.1103 0.0824 0.8073 5 A 0.2000 0.1943 0.6058 6 G 0.3428 0.1591 0.4981 7 L 0.5352 0.1842 0.2806 8 Y 0.6164 0.1738 0.2098 9 A 0.6290 0.1654 0.2056 10 F 0.5412 0.1757 0.2831 11 N 0.3430 0.1634 0.4937 12 S 0.1632 0.1721 0.6647 13 G 0.1201 0.1114 0.7685 14 G 0.2296 0.0825 0.6879 15 I 0.4747 0.0524 0.4729 16 S 0.5948 0.0499 0.3553 17 L 0.4742 0.1779 0.3478 18 D 0.3845 0.2184 0.3970 19 L 0.2408 0.2594 0.4998 20 G 0.1981 0.1110 0.6909 21 I 0.2225 0.0796 0.6980 22 N 0.1856 0.0623 0.7521 23 D 0.1207 0.0208 0.8585 24 P 0.1535 0.0216 0.8249 25 V 0.2652 0.0163 0.7186 26 P 0.2767 0.0238 0.6995 27 F 0.2826 0.1062 0.6112 28 N 0.2544 0.1286 0.6170 29 T 0.2658 0.1785 0.5557 30 V 0.2430 0.2184 0.5386 31 G 0.1459 0.2009 0.6532 32 S 0.1133 0.2820 0.6047 33 Q 0.1278 0.3652 0.5070 34 F 0.1229 0.4274 0.4496 35 G 0.1258 0.4054 0.4688 36 T 0.1735 0.4498 0.3767 37 A 0.1940 0.5381 0.2679 38 I 0.1480 0.6053 0.2467 39 S 0.1579 0.5306 0.3114 40 Q 0.1607 0.4189 0.4204 41 L 0.2288 0.1800 0.5912 42 D 0.1353 0.0316 0.8331 43 A 0.0259 0.2336 0.7406 44 D 0.0526 0.1805 0.7669 45 T 0.3231 0.1505 0.5264 46 F 0.7896 0.0260 0.1844 47 V 0.8867 0.0129 0.1003 48 I 0.8586 0.0162 0.1252 49 S 0.6476 0.0465 0.3059 50 E 0.3367 0.0734 0.5899 51 T 0.1950 0.0609 0.7441 52 G 0.2377 0.0596 0.7027 53 F 0.6007 0.0423 0.3570 54 Y 0.8128 0.0304 0.1568 55 K 0.8664 0.0200 0.1136 56 I 0.8906 0.0170 0.0924 57 T 0.9051 0.0210 0.0739 58 V 0.9011 0.0272 0.0718 59 I 0.8586 0.0553 0.0861 60 A 0.6918 0.1348 0.1734 61 N 0.4326 0.1750 0.3924 62 T 0.2725 0.2513 0.4762 63 A 0.2850 0.2945 0.4205 64 T 0.4131 0.2902 0.2968 65 A 0.5253 0.2731 0.2016 66 S 0.5513 0.2510 0.1977 67 V 0.5926 0.2091 0.1984 68 L 0.5069 0.1486 0.3444 69 G 0.2907 0.0606 0.6486 70 G 0.2942 0.0435 0.6623 71 L 0.6393 0.0173 0.3434 72 T 0.8537 0.0088 0.1375 73 I 0.9011 0.0052 0.0937 74 Q 0.8913 0.0062 0.1025 75 V 0.7927 0.0287 0.1786 76 N 0.3192 0.0235 0.6573 77 G 0.1970 0.0262 0.7768 78 V 0.5195 0.0107 0.4698 79 P 0.6074 0.0101 0.3825 80 V 0.2994 0.0190 0.6816 81 P 0.1217 0.0442 0.8341 82 G 0.0841 0.0485 0.8674 83 T 0.1305 0.0523 0.8172 84 G 0.1305 0.0717 0.7978 85 S 0.2440 0.1220 0.6340 86 S 0.3601 0.1395 0.5004 87 L 0.5940 0.1509 0.2551 88 I 0.6402 0.1305 0.2293 89 S 0.5255 0.1350 0.3394 90 L 0.2221 0.1901 0.5878 91 G 0.0903 0.1036 0.8062 92 A 0.1329 0.1351 0.7320 93 P 0.2017 0.2138 0.5845 94 I 0.6394 0.1999 0.1607 95 V 0.6556 0.2785 0.0659 96 I 0.6611 0.2819 0.0570 97 Q 0.6407 0.2794 0.0798 98 A 0.5924 0.2891 0.1185 99 I 0.4795 0.3393 0.1812 100 T 0.3677 0.3987 0.2336 101 Q 0.3185 0.3990 0.2825 102 I 0.3079 0.3004 0.3918 103 T 0.2115 0.1898 0.5987 104 T 0.1466 0.1398 0.7136 105 T 0.0885 0.0659 0.8457 106 P 0.0567 0.3413 0.6020 107 S 0.1207 0.3081 0.5711 108 L 0.2638 0.4772 0.2590 109 V 0.4650 0.3746 0.1604 110 E 0.5971 0.3111 0.0918 111 V 0.6963 0.2210 0.0827 112 I 0.6574 0.2590 0.0836 113 V 0.5934 0.2672 0.1394 114 T 0.3452 0.2962 0.3586 115 G 0.1723 0.2116 0.6161 116 L 0.1337 0.2717 0.5946 117 G 0.2204 0.2493 0.5304 118 L 0.3651 0.3133 0.3216 119 S 0.4277 0.3145 0.2578 120 L 0.3405 0.4475 0.2119 121 A 0.3320 0.3880 0.2800 122 L 0.1894 0.3298 0.4808 123 G 0.1076 0.1282 0.7642 124 T 0.1237 0.1631 0.7133 125 S 0.1480 0.3115 0.5405 126 A 0.1077 0.6578 0.2344 127 S 0.1390 0.7232 0.1378 128 I 0.2130 0.7048 0.0821 129 I 0.1282 0.8100 0.0619 130 I 0.1100 0.8330 0.0570 131 E 0.0849 0.8544 0.0606 132 K 0.0705 0.8599 0.0696 133 V 0.0609 0.8398 0.0993 134 A 0.0596 0.7884 0.1520 135 H 0.0597 0.6896 0.2507 136 H 0.0582 0.5212 0.4207 137 H 0.0663 0.3294 0.6043 138 H 0.0640 0.2153 0.7208 139 H 0.0703 0.1285 0.8012 140 H 0.0540 0.0544 0.8917