# This file is the result of combining several RDB files, specifically # T0151.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0151.t2k.stride-ebghtl.rdb (weight 1.24869) # T0151.t2k.str.rdb (weight 1.53983) # T0151.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 T0151.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0151 # 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 T0151.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 147 # # ============================================ # Comments from T0151.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0151 # 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 T0151.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 147 # # ============================================ # Comments from T0151.t2k.str.rdb # ============================================ # TARGET T0151 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0151.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 147 # # ============================================ # Comments from T0151.t2k.alpha.rdb # ============================================ # TARGET T0151 # 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 T0151.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 147 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0737 0.1135 0.8128 2 A 0.1127 0.1536 0.7337 3 G 0.1581 0.1370 0.7049 4 D 0.2409 0.0706 0.6885 5 T 0.3310 0.0300 0.6390 6 T 0.7237 0.0215 0.2549 7 I 0.9124 0.0045 0.0831 8 T 0.9221 0.0054 0.0725 9 I 0.9151 0.0036 0.0813 10 V 0.8149 0.0221 0.1630 11 G 0.6970 0.0228 0.2802 12 N 0.5796 0.0427 0.3777 13 L 0.3701 0.0865 0.5434 14 T 0.2519 0.0729 0.6753 15 A 0.1598 0.0606 0.7796 16 D 0.1143 0.0238 0.8620 17 P 0.0857 0.2509 0.6634 18 E 0.2462 0.2428 0.5109 19 L 0.5728 0.1408 0.2864 20 R 0.6678 0.0568 0.2754 21 F 0.7635 0.0220 0.2145 22 T 0.2816 0.0221 0.6963 23 P 0.0458 0.1112 0.8430 24 S 0.0495 0.0239 0.9266 25 G 0.0436 0.0312 0.9252 26 A 0.2556 0.0125 0.7318 27 A 0.7671 0.0043 0.2286 28 V 0.8868 0.0053 0.1079 29 A 0.9183 0.0043 0.0775 30 N 0.9241 0.0039 0.0720 31 F 0.9243 0.0037 0.0720 32 T 0.9199 0.0040 0.0761 33 V 0.8957 0.0055 0.0988 34 A 0.7969 0.0128 0.1903 35 S 0.6648 0.0154 0.3197 36 T 0.4157 0.0226 0.5617 37 P 0.2278 0.1204 0.6518 38 R 0.2502 0.1488 0.6011 39 I 0.2857 0.1590 0.5553 40 Y 0.3196 0.1013 0.5790 41 D 0.2067 0.0953 0.6979 42 R 0.0519 0.1552 0.7930 43 Q 0.0498 0.0981 0.8521 44 T 0.0604 0.0862 0.8534 45 G 0.1063 0.1034 0.7904 46 E 0.3707 0.1181 0.5112 47 W 0.5069 0.1370 0.3561 48 K 0.4631 0.1736 0.3632 49 D 0.3761 0.1696 0.4543 50 G 0.2921 0.1300 0.5779 51 E 0.3497 0.0634 0.5869 52 A 0.4598 0.0508 0.4894 53 L 0.6001 0.0594 0.3404 54 F 0.7604 0.0510 0.1887 55 L 0.8169 0.0310 0.1521 56 R 0.8379 0.0326 0.1295 57 C 0.8539 0.0294 0.1167 58 N 0.8578 0.0272 0.1150 59 I 0.7319 0.0593 0.2088 60 W 0.3404 0.1530 0.5066 61 R 0.0757 0.3586 0.5658 62 E 0.0445 0.6039 0.3516 63 A 0.0161 0.8581 0.1258 64 A 0.0075 0.9210 0.0715 65 E 0.0060 0.9395 0.0545 66 N 0.0067 0.9339 0.0594 67 V 0.0062 0.9286 0.0652 68 A 0.0070 0.9279 0.0651 69 E 0.0077 0.8972 0.0952 70 S 0.0112 0.8207 0.1681 71 L 0.0446 0.6157 0.3397 72 T 0.0413 0.3758 0.5829 73 R 0.0394 0.1752 0.7854 74 G 0.0425 0.0451 0.9125 75 A 0.1384 0.0201 0.8416 76 R 0.6433 0.0054 0.3513 77 V 0.8738 0.0046 0.1216 78 I 0.9139 0.0038 0.0824 79 V 0.9074 0.0044 0.0882 80 S 0.8291 0.0198 0.1511 81 G 0.8302 0.0075 0.1623 82 R 0.8576 0.0070 0.1354 83 L 0.8458 0.0062 0.1480 84 K 0.8214 0.0158 0.1628 85 Q 0.8064 0.0104 0.1833 86 R 0.6247 0.0225 0.3528 87 S 0.6966 0.0139 0.2895 88 F 0.7443 0.0160 0.2397 89 E 0.7732 0.0159 0.2109 90 T 0.3786 0.0313 0.5901 91 R 0.0764 0.1160 0.8076 92 E 0.0650 0.0276 0.9074 93 G 0.0893 0.0301 0.8806 94 E 0.4619 0.0095 0.5286 95 K 0.8736 0.0039 0.1225 96 R 0.8492 0.0080 0.1427 97 T 0.8735 0.0055 0.1210 98 V 0.8640 0.0054 0.1307 99 I 0.8896 0.0057 0.1047 100 E 0.9218 0.0037 0.0744 101 V 0.9221 0.0037 0.0742 102 E 0.9100 0.0059 0.0842 103 V 0.8729 0.0118 0.1153 104 D 0.7400 0.0439 0.2161 105 E 0.7284 0.0400 0.2316 106 I 0.6818 0.0445 0.2737 107 G 0.6712 0.0556 0.2732 108 P 0.5360 0.1163 0.3477 109 S 0.3115 0.1970 0.4915 110 L 0.1961 0.2230 0.5809 111 R 0.1305 0.2527 0.6168 112 Y 0.1128 0.2820 0.6052 113 A 0.0881 0.2769 0.6350 114 T 0.0849 0.2659 0.6492 115 A 0.0902 0.2685 0.6413 116 K 0.0909 0.2354 0.6737 117 V 0.0996 0.2124 0.6880 118 N 0.1073 0.1828 0.7099 119 K 0.1186 0.1712 0.7102 120 A 0.1112 0.2016 0.6872 121 S 0.1105 0.1823 0.7072 122 R 0.1159 0.1981 0.6860 123 S 0.1135 0.1882 0.6983 124 G 0.1094 0.1934 0.6973 125 G 0.1203 0.1804 0.6993 126 F 0.1221 0.1985 0.6794 127 G 0.1108 0.1760 0.7132 128 S 0.1186 0.1616 0.7198 129 G 0.1128 0.1770 0.7102 130 S 0.1159 0.1654 0.7186 131 R 0.1118 0.1768 0.7114 132 P 0.0993 0.1944 0.7063 133 A 0.0916 0.1860 0.7224 134 P 0.0875 0.2097 0.7028 135 A 0.0822 0.2361 0.6817 136 Q 0.0768 0.2345 0.6887 137 T 0.0871 0.2101 0.7027 138 S 0.0861 0.2425 0.6713 139 S 0.0795 0.2603 0.6602 140 A 0.0717 0.2619 0.6664 141 S 0.0688 0.2377 0.6935 142 G 0.0691 0.2202 0.7106 143 D 0.0796 0.1904 0.7301 144 D 0.0713 0.1743 0.7544 145 P 0.0711 0.1903 0.7385 146 W 0.0768 0.1924 0.7307 147 G 0.0725 0.2237 0.7038 148 S 0.0808 0.2027 0.7165 149 A 0.0782 0.1874 0.7343 150 P 0.0691 0.1628 0.7681 151 A 0.0514 0.1883 0.7603 152 S 0.0576 0.1556 0.7868 153 G 0.0729 0.1265 0.8005 154 S 0.1023 0.1579 0.7399 155 F 0.1142 0.1627 0.7231 156 G 0.1207 0.1451 0.7343 157 G 0.0980 0.1888 0.7133 158 G 0.0750 0.2044 0.7206 159 D 0.0622 0.2587 0.6791 160 D 0.0391 0.2215 0.7394 161 E 0.0667 0.1565 0.7769 162 P 0.1043 0.0704 0.8253 163 P 0.0977 0.0482 0.8541 164 F 0.0588 0.0266 0.9146