# This file is the result of combining several RDB files, specifically # T0144.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0144.t2k.stride-ebghtl.rdb (weight 1.24869) # T0144.t2k.str.rdb (weight 1.53983) # T0144.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 T0144.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0144 # 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 T0144.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 396 # # ============================================ # Comments from T0144.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0144 # 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 T0144.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 396 # # ============================================ # Comments from T0144.t2k.str.rdb # ============================================ # TARGET T0144 # 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 T0144.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 396 # # ============================================ # Comments from T0144.t2k.alpha.rdb # ============================================ # TARGET T0144 # 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 T0144.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 396 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0598 0.0251 0.9151 2 S 0.1819 0.0277 0.7904 3 N 0.1178 0.0220 0.8602 4 P 0.1581 0.0657 0.7763 5 K 0.5494 0.0415 0.4091 6 V 0.8298 0.0158 0.1543 7 F 0.8481 0.0201 0.1318 8 F 0.8481 0.0157 0.1362 9 D 0.7832 0.0190 0.1978 10 M 0.7499 0.0235 0.2266 11 A 0.7441 0.0264 0.2295 12 I 0.6253 0.0426 0.3321 13 A 0.2562 0.0438 0.7000 14 G 0.2108 0.0452 0.7440 15 N 0.4232 0.0166 0.5602 16 P 0.5964 0.0280 0.3756 17 A 0.6204 0.0356 0.3440 18 G 0.6016 0.0257 0.3727 19 R 0.8207 0.0083 0.1710 20 I 0.8962 0.0044 0.0994 21 V 0.9156 0.0057 0.0788 22 M 0.9144 0.0062 0.0794 23 E 0.9010 0.0072 0.0919 24 L 0.8070 0.0159 0.1771 25 Y 0.4641 0.0460 0.4899 26 A 0.0701 0.4406 0.4894 27 D 0.0274 0.4110 0.5615 28 T 0.0652 0.3656 0.5692 29 T 0.0802 0.1368 0.7831 30 P 0.0414 0.6714 0.2872 31 R 0.0184 0.8546 0.1269 32 T 0.0098 0.9175 0.0727 33 A 0.0056 0.9498 0.0446 34 E 0.0051 0.9537 0.0412 35 N 0.0055 0.9446 0.0498 36 F 0.0045 0.9498 0.0456 37 R 0.0048 0.9487 0.0465 38 A 0.0055 0.9398 0.0548 39 L 0.0081 0.9118 0.0801 40 C 0.0301 0.7889 0.1810 41 T 0.0357 0.4723 0.4919 42 G 0.0498 0.1535 0.7967 43 E 0.0970 0.1324 0.7706 44 K 0.1784 0.1155 0.7062 45 G 0.1934 0.0933 0.7133 46 V 0.2695 0.0729 0.6575 47 G 0.1439 0.0827 0.7734 48 R 0.0669 0.1303 0.8027 49 S 0.0522 0.0716 0.8762 50 G 0.0684 0.0591 0.8724 51 K 0.2393 0.0293 0.7314 52 P 0.4879 0.0359 0.4762 53 L 0.3607 0.0629 0.5764 54 H 0.2865 0.0737 0.6398 55 Y 0.2428 0.0765 0.6807 56 K 0.1490 0.1032 0.7478 57 G 0.1408 0.0704 0.7888 58 S 0.2999 0.0490 0.6512 59 T 0.5366 0.0818 0.3816 60 F 0.6359 0.1103 0.2538 61 H 0.6678 0.1156 0.2165 62 R 0.6944 0.0996 0.2060 63 V 0.6457 0.0934 0.2609 64 I 0.4454 0.0481 0.5065 65 P 0.1397 0.1228 0.7375 66 N 0.1061 0.1035 0.7904 67 F 0.4707 0.0644 0.4649 68 M 0.7377 0.0293 0.2331 69 C 0.7519 0.0272 0.2209 70 Q 0.5864 0.0406 0.3730 71 G 0.3386 0.0441 0.6173 72 G 0.2111 0.0406 0.7483 73 D 0.1656 0.0418 0.7926 74 F 0.1159 0.0951 0.7890 75 T 0.1397 0.1005 0.7598 76 A 0.1106 0.0925 0.7969 77 G 0.1035 0.0802 0.8164 78 N 0.1109 0.0765 0.8126 79 G 0.0935 0.0680 0.8385 80 T 0.1088 0.0715 0.8196 81 G 0.0982 0.0651 0.8367 82 A 0.1266 0.0960 0.7774 83 E 0.2482 0.1243 0.6275 84 S 0.2963 0.1583 0.5454 85 I 0.2626 0.1950 0.5424 86 Y 0.1738 0.1536 0.6726 87 G 0.1111 0.1230 0.7659 88 A 0.1644 0.1100 0.7256 89 K 0.2591 0.1246 0.6163 90 F 0.2406 0.1220 0.6374 91 A 0.1649 0.1457 0.6895 92 D 0.1415 0.1683 0.6903 93 E 0.0871 0.3040 0.6089 94 N 0.1029 0.2594 0.6377 95 F 0.1535 0.1957 0.6508 96 I 0.1448 0.2014 0.6538 97 K 0.1692 0.1757 0.6552 98 R 0.1762 0.1368 0.6870 99 H 0.1780 0.1020 0.7201 100 T 0.1316 0.0742 0.7941 101 G 0.0959 0.0487 0.8554 102 P 0.1140 0.0902 0.7958 103 G 0.3425 0.0622 0.5953 104 I 0.7131 0.0519 0.2351 105 L 0.7880 0.0380 0.1741 106 S 0.7527 0.0581 0.1892 107 M 0.7176 0.0919 0.1904 108 A 0.5893 0.1075 0.3032 109 N 0.3839 0.0996 0.5165 110 A 0.2237 0.0571 0.7192 111 G 0.1049 0.0339 0.8612 112 A 0.0762 0.0805 0.8433 113 G 0.0868 0.0784 0.8348 114 T 0.0842 0.1030 0.8128 115 N 0.0986 0.0777 0.8237 116 G 0.1213 0.0900 0.7887 117 S 0.3541 0.0336 0.6123 118 Q 0.7185 0.0205 0.2610 119 F 0.8642 0.0084 0.1274 120 F 0.8794 0.0108 0.1098 121 I 0.8799 0.0103 0.1099 122 C 0.8316 0.0132 0.1552 123 T 0.6222 0.0277 0.3500 124 E 0.3796 0.0218 0.5986 125 K 0.2058 0.0347 0.7595 126 T 0.1701 0.0482 0.7816 127 E 0.1418 0.1995 0.6587 128 W 0.1399 0.2254 0.6347 129 L 0.1344 0.1694 0.6962 130 D 0.0883 0.0746 0.8372 131 G 0.0586 0.0751 0.8662 132 K 0.1715 0.0587 0.7697 133 H 0.6824 0.0151 0.3025 134 V 0.8011 0.0055 0.1934 135 V 0.8612 0.0094 0.1294 136 F 0.7902 0.0290 0.1807 137 G 0.7386 0.0354 0.2259 138 K 0.7307 0.0451 0.2242 139 V 0.6133 0.0801 0.3065 140 I 0.3486 0.1600 0.4914 141 E 0.1257 0.2657 0.6086 142 G 0.0642 0.3141 0.6216 143 M 0.0562 0.6343 0.3096 144 N 0.0624 0.7652 0.1724 145 V 0.0094 0.9306 0.0600 146 V 0.0068 0.9452 0.0479 147 R 0.0070 0.9495 0.0435 148 D 0.0069 0.9467 0.0465 149 I 0.0073 0.9355 0.0572 150 E 0.0076 0.9090 0.0834 151 K 0.0157 0.7751 0.2092 152 V 0.0658 0.4329 0.5013 153 G 0.0943 0.0874 0.8183 154 S 0.0784 0.0624 0.8593 155 G 0.0417 0.1203 0.8380 156 S 0.0514 0.0597 0.8889 157 G 0.0377 0.0568 0.9055 158 K 0.1536 0.0221 0.8243 159 T 0.3575 0.0135 0.6290 160 S 0.3004 0.0332 0.6664 161 R 0.3722 0.0175 0.6103 162 P 0.4608 0.0121 0.5271 163 V 0.7209 0.0060 0.2730 164 T 0.8620 0.0073 0.1307 165 I 0.8488 0.0125 0.1387 166 A 0.6435 0.0395 0.3170 167 D 0.4641 0.0258 0.5101 168 C 0.2706 0.0533 0.6761 169 G 0.3491 0.0579 0.5930 170 Q 0.4208 0.0516 0.5276 171 L 0.2190 0.0460 0.7350 172 S 0.0552 0.0217 0.9231