# This file is the result of combining several RDB files, specifically # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 338 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 338 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0316.t2k-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 22.7135 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 338 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.1260 0.1362 0.7379 2 G 0.1074 0.1550 0.7376 3 H 0.0960 0.2116 0.6924 4 L 0.0947 0.1934 0.7119 5 E 0.0756 0.1723 0.7520 6 K 0.0342 0.5851 0.3807 7 P 0.0062 0.8530 0.1409 8 E 0.0071 0.9259 0.0670 9 V 0.0058 0.9479 0.0463 10 R 0.0047 0.9542 0.0411 11 R 0.0048 0.9600 0.0352 12 L 0.0047 0.9603 0.0350 13 A 0.0047 0.9588 0.0364 14 E 0.0050 0.9521 0.0430 15 E 0.0056 0.9301 0.0643 16 A 0.0417 0.5263 0.4320 17 G 0.0327 0.0345 0.9328 18 L 0.0648 0.0330 0.9022 19 S 0.2025 0.0992 0.6983 20 T 0.3215 0.2191 0.4594 21 A 0.3547 0.1749 0.4704 22 K 0.2867 0.0801 0.6332 23 K 0.1911 0.0712 0.7377 24 K 0.0875 0.2308 0.6817 25 D 0.1011 0.1806 0.7183 26 S 0.2576 0.1297 0.6127 27 T 0.2608 0.0709 0.6683 28 G 0.3508 0.0604 0.5888 29 I 0.6998 0.0300 0.2702 30 C 0.7452 0.0247 0.2301 31 F 0.7450 0.0165 0.2385 32 I 0.5200 0.0230 0.4569 33 G 0.1889 0.0275 0.7836 34 E 0.0598 0.1390 0.8011 35 K 0.0503 0.1745 0.7752 36 N 0.0912 0.2451 0.6637 37 F 0.0241 0.8272 0.1487 38 K 0.0069 0.9122 0.0809 39 N 0.0079 0.9045 0.0876 40 F 0.0193 0.8918 0.0889 41 L 0.0152 0.8680 0.1168 42 S 0.0086 0.7999 0.1914 43 N 0.0156 0.6900 0.2944 44 Y 0.0449 0.4380 0.5171 45 L 0.0648 0.0843 0.8509 46 P 0.0767 0.0382 0.8851 47 A 0.1055 0.0571 0.8374 48 Q 0.1308 0.0354 0.8338 49 P 0.2519 0.0407 0.7074 50 G 0.3941 0.0256 0.5803 51 R 0.7204 0.0079 0.2717 52 M 0.8385 0.0053 0.1562 53 M 0.8492 0.0050 0.1458 54 T 0.4741 0.0107 0.5152 55 V 0.1168 0.1081 0.7751 56 D 0.0530 0.0170 0.9300 57 G 0.0588 0.0267 0.9145 58 R 0.4234 0.0083 0.5683 59 D 0.8809 0.0031 0.1160 60 M 0.8250 0.0184 0.1566 61 G 0.8178 0.0144 0.1678 62 E 0.6794 0.0323 0.2884 63 H 0.5509 0.0408 0.4082 64 A 0.3383 0.0713 0.5904 65 G 0.4254 0.0690 0.5057 66 L 0.6554 0.0582 0.2864 67 M 0.7010 0.0686 0.2304 68 Y 0.7180 0.0709 0.2111 69 Y 0.6642 0.0666 0.2692 70 T 0.5655 0.0749 0.3596 71 I 0.4515 0.1941 0.3544 72 G 0.3773 0.2006 0.4221 73 Q 0.3312 0.2597 0.4091 74 R 0.2994 0.2626 0.4380 75 G 0.1685 0.2516 0.5799 76 G 0.1385 0.1471 0.7144 77 L 0.1890 0.1025 0.7085 78 G 0.2355 0.0667 0.6978 79 I 0.2240 0.1233 0.6528 80 G 0.1683 0.1445 0.6873 81 G 0.1326 0.1240 0.7434 82 Q 0.1036 0.1709 0.7255 83 H 0.0691 0.1722 0.7587 84 G 0.0586 0.1653 0.7761 85 G 0.0646 0.1445 0.7909 86 D 0.0963 0.1148 0.7890 87 N 0.1393 0.0643 0.7964 88 A 0.1986 0.0235 0.7779 89 P 0.3853 0.0181 0.5966 90 W 0.7692 0.0184 0.2123 91 F 0.8850 0.0084 0.1066 92 V 0.9046 0.0055 0.0899 93 V 0.8389 0.0247 0.1364 94 G 0.8408 0.0092 0.1499 95 K 0.6930 0.0163 0.2908 96 D 0.4938 0.0258 0.4804 97 L 0.0904 0.2962 0.6134 98 S 0.0708 0.2444 0.6848 99 K 0.1070 0.1985 0.6945 100 N 0.1978 0.0327 0.7695 101 I 0.7832 0.0074 0.2094 102 L 0.9218 0.0034 0.0748 103 Y 0.9226 0.0033 0.0741 104 V 0.8707 0.0108 0.1185 105 G 0.5637 0.0075 0.4289 106 Q 0.1740 0.0412 0.7848 107 G 0.0294 0.2354 0.7352 108 F 0.0227 0.3761 0.6012 109 Y 0.0359 0.3459 0.6182 110 H 0.0672 0.2784 0.6544 111 D 0.0289 0.4738 0.4973 112 S 0.0556 0.5747 0.3696 113 L 0.1136 0.5459 0.3405 114 M 0.2190 0.4454 0.3356 115 S 0.2924 0.4051 0.3025 116 T 0.3117 0.4282 0.2600 117 S 0.3929 0.3577 0.2493 118 L 0.3949 0.3073 0.2977 119 E 0.4686 0.2019 0.3296 120 A 0.4095 0.1753 0.4152 121 S 0.2330 0.1857 0.5812 122 Q 0.2548 0.2162 0.5289 123 V 0.4947 0.1289 0.3764 124 H 0.5623 0.0982 0.3395 125 F 0.4742 0.1217 0.4041 126 T 0.2747 0.1463 0.5790 127 R 0.1218 0.1521 0.7261 128 E 0.0802 0.1013 0.8186 129 M 0.0924 0.0473 0.8603 130 P 0.0569 0.0407 0.9025