# This file is the result of combining several RDB files, specifically # T0618.t04.str2.rdb (weight 1.54425) # T0618.t04.str4.rdb (weight 0.924988) # T0618.t04.pb.rdb (weight 0.789901) # T0618.t04.bys.rdb (weight 0.748322) # T0618.t04.alpha.rdb (weight 0.678173) # 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 T0618.t04.str2.rdb # ============================================ # TARGET T0618 # Using neural net dunbrack-40pc-3157-t04-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 T0618.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 41.1144 # # ============================================ # Comments from T0618.t04.str4.rdb # ============================================ # TARGET T0618 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0618.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 41.1144 # # ============================================ # Comments from T0618.t04.pb.rdb # ============================================ # TARGET T0618 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0618.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 41.1144 # # ============================================ # Comments from T0618.t04.bys.rdb # ============================================ # TARGET T0618 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0618.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 41.1144 # # ============================================ # Comments from T0618.t04.alpha.rdb # ============================================ # TARGET T0618 # Using neural net dunbrack-40pc-3157-t04-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 T0618.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 41.1144 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2255 0.1594 0.6151 2 K 0.1772 0.1796 0.6431 3 K 0.1394 0.4025 0.4581 4 E 0.1468 0.3885 0.4646 5 S 0.1764 0.2928 0.5308 6 Q 0.2216 0.2513 0.5272 7 V 0.3159 0.2163 0.4678 8 I 0.2882 0.2063 0.5055 9 F 0.2607 0.1370 0.6024 10 D 0.1848 0.1117 0.7034 11 K 0.0406 0.5473 0.4121 12 N 0.0608 0.5190 0.4202 13 V 0.0190 0.7825 0.1985 14 I 0.0114 0.8602 0.1284 15 E 0.0092 0.9111 0.0797 16 F 0.0098 0.9157 0.0745 17 V 0.0086 0.9215 0.0699 18 T 0.0086 0.9233 0.0682 19 V 0.0087 0.9214 0.0699 20 A 0.0083 0.9222 0.0695 21 A 0.0083 0.9233 0.0684 22 E 0.0084 0.9220 0.0696 23 F 0.0084 0.9204 0.0712 24 C 0.0084 0.9195 0.0722 25 A 0.0084 0.9152 0.0763 26 F 0.0094 0.9088 0.0819 27 L 0.0138 0.8936 0.0926 28 E 0.0182 0.8609 0.1209 29 R 0.0418 0.7563 0.2019 30 A 0.0249 0.7699 0.2051 31 E 0.0206 0.7888 0.1906 32 S 0.0280 0.7802 0.1917 33 M 0.0480 0.7372 0.2148 34 K 0.0576 0.6417 0.3006 35 R 0.0640 0.5725 0.3635 36 S 0.0406 0.6047 0.3547 37 T 0.0376 0.6298 0.3326 38 F 0.0459 0.7058 0.2484 39 V 0.0194 0.8265 0.1541 40 D 0.0121 0.8880 0.1000 41 T 0.0098 0.8958 0.0945 42 T 0.0106 0.8831 0.1064 43 L 0.0095 0.8890 0.1015 44 K 0.0091 0.8541 0.1367 45 I 0.0122 0.8145 0.1733 46 L 0.0176 0.7941 0.1883 47 P 0.0099 0.8683 0.1217 48 L 0.0098 0.8976 0.0926 49 L 0.0109 0.9062 0.0830 50 Y 0.0133 0.8996 0.0871 51 L 0.0135 0.8956 0.0909 52 K 0.0205 0.8523 0.1273 53 A 0.0253 0.7970 0.1777 54 S 0.0388 0.6531 0.3081 55 M 0.0675 0.4083 0.5243 56 L 0.1585 0.1602 0.6813 57 P 0.1168 0.2559 0.6273 58 K 0.1077 0.3833 0.5090 59 C 0.2118 0.2341 0.5541 60 E 0.2960 0.1607 0.5433 61 M 0.3005 0.1482 0.5514 62 I 0.2201 0.1047 0.6752 63 G 0.1508 0.1269 0.7223 64 D 0.1189 0.2682 0.6129 65 E 0.1444 0.2093 0.6463 66 S 0.2212 0.0712 0.7076 67 P 0.1789 0.1970 0.6241 68 E 0.2352 0.2226 0.5423 69 T 0.2520 0.1672 0.5809 70 Y 0.2430 0.1240 0.6331 71 V 0.2631 0.0688 0.6681 72 T 0.1854 0.0478 0.7668 73 E 0.0380 0.6171 0.3449 74 E 0.0195 0.7730 0.2075 75 I 0.0201 0.8266 0.1533 76 Y 0.0164 0.8725 0.1111 77 E 0.0112 0.9090 0.0799 78 V 0.0107 0.9180 0.0714 79 L 0.0086 0.9208 0.0707 80 R 0.0085 0.9229 0.0686 81 I 0.0084 0.9221 0.0694 82 N 0.0097 0.9125 0.0778 83 L 0.0091 0.8971 0.0938 84 A 0.0090 0.9057 0.0853 85 S 0.0098 0.8726 0.1176 86 I 0.0162 0.7338 0.2500 87 L 0.0487 0.5443 0.4070 88 A 0.0655 0.4071 0.5274 89 E 0.0690 0.3706 0.5604 90 K 0.0901 0.3233 0.5866 91 D 0.1132 0.2876 0.5992 92 D 0.0901 0.5010 0.4088 93 Y 0.1624 0.4631 0.3745 94 L 0.2647 0.4110 0.3243 95 E 0.3996 0.3070 0.2933 96 V 0.4854 0.1951 0.3195 97 F 0.4129 0.1079 0.4792 98 L 0.2875 0.0756 0.6369 99 P 0.1613 0.1638 0.6749 100 D 0.1052 0.3779 0.5169 101 M 0.1125 0.3921 0.4954 102 A 0.1582 0.2831 0.5587 103 Y 0.1603 0.2289 0.6108 104 S 0.1367 0.2324 0.6310 105 D 0.1362 0.1943 0.6695 106 E 0.2545 0.0881 0.6574 107 P 0.2384 0.1182 0.6434 108 I 0.2173 0.2530 0.5297 109 K 0.1721 0.3381 0.4898 110 K 0.1371 0.3755 0.4875 111 N 0.1646 0.2738 0.5616 112 I 0.1569 0.3364 0.5066 113 S 0.1340 0.4184 0.4476 114 E 0.0317 0.6822 0.2861 115 D 0.0474 0.6646 0.2880 116 L 0.0149 0.7927 0.1924 117 A 0.0096 0.8665 0.1239 118 D 0.0091 0.9027 0.0882 119 I 0.0086 0.9107 0.0807 120 Y 0.0088 0.9161 0.0750 121 Q 0.0092 0.9085 0.0823 122 D 0.0145 0.8919 0.0935 123 I 0.0094 0.8946 0.0960 124 K 0.0089 0.8967 0.0944 125 D 0.0105 0.8859 0.1036 126 F 0.0141 0.8935 0.0924 127 I 0.0202 0.8893 0.0905 128 F 0.0272 0.8834 0.0894 129 V 0.0494 0.8424 0.1081 130 F 0.0718 0.7751 0.1531 131 Q 0.0717 0.6925 0.2357 132 L 0.0707 0.4489 0.4804 133 G 0.0566 0.1736 0.7698 134 L 0.1015 0.2555 0.6431 135 N 0.0646 0.4168 0.5186 136 E 0.0361 0.6754 0.2886 137 T 0.0398 0.7185 0.2417 138 M 0.0204 0.8321 0.1474 139 N 0.0109 0.8905 0.0987 140 D 0.0092 0.9099 0.0810 141 S 0.0096 0.9159 0.0745 142 L 0.0091 0.9173 0.0736 143 A 0.0092 0.9189 0.0719 144 I 0.0117 0.9117 0.0766 145 C 0.0204 0.8889 0.0907 146 Q 0.0206 0.8775 0.1018 147 E 0.0197 0.8543 0.1260 148 N 0.0405 0.7146 0.2449 149 F 0.0498 0.6553 0.2949 150 G 0.0489 0.7322 0.2189 151 L 0.0420 0.7951 0.1630 152 L 0.0410 0.7828 0.1761 153 W 0.0300 0.7981 0.1719 154 G 0.0109 0.8942 0.0949 155 Q 0.0085 0.9139 0.0776 156 K 0.0087 0.9177 0.0736 157 L 0.0083 0.9231 0.0686 158 V 0.0083 0.9227 0.0690 159 N 0.0083 0.9202 0.0715 160 T 0.0083 0.9237 0.0680 161 M 0.0083 0.9220 0.0697 162 R 0.0083 0.9101 0.0816 163 A 0.0084 0.9108 0.0808 164 L 0.0087 0.9010 0.0903 165 H 0.0092 0.8672 0.1236 166 D 0.0150 0.8056 0.1793 167 V 0.0383 0.7315 0.2302 168 K 0.0882 0.5452 0.3666 169 Y 0.1332 0.3382 0.5286 170 S 0.1670 0.1244 0.7086 171 P 0.0481 0.4746 0.4773 172 K 0.0744 0.4605 0.4651 173 A 0.1568 0.3333 0.5099 174 R 0.1734 0.2159 0.6107 175 L 0.1745 0.3389 0.4866 176 E 0.1289 0.3822 0.4888 177 H 0.1415 0.3297 0.5288 178 H 0.1418 0.2646 0.5936 179 H 0.1896 0.2469 0.5635 180 H 0.2110 0.2191 0.5699 181 H 0.1948 0.1893 0.6159 182 H 0.1867 0.1493 0.6639