# This file is the result of combining several RDB files, specifically # T0277.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0277.t2k.stride-ebghtl.rdb (weight 1.24869) # T0277.t2k.str2.rdb (weight 1.54758) # T0277.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 T0277.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0277 # 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 T0277.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 19 # # ============================================ # Comments from T0277.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0277 # 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 T0277.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 19 # # ============================================ # Comments from T0277.t2k.str2.rdb # ============================================ # TARGET T0277 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0277.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 19 # # ============================================ # Comments from T0277.t2k.alpha.rdb # ============================================ # TARGET T0277 # 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 T0277.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 19 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0172 0.4818 0.5010 2 A 0.0137 0.7456 0.2407 3 S 0.0120 0.7721 0.2159 4 L 0.0048 0.9288 0.0664 5 A 0.0048 0.9511 0.0441 6 R 0.0047 0.9546 0.0407 7 A 0.0047 0.9561 0.0391 8 V 0.0048 0.9550 0.0402 9 E 0.0048 0.9499 0.0453 10 R 0.0050 0.9410 0.0539 11 L 0.0057 0.9248 0.0695 12 K 0.0062 0.8938 0.1000 13 A 0.0079 0.8024 0.1897 14 A 0.0183 0.6785 0.3032 15 L 0.0270 0.5183 0.4547 16 E 0.0279 0.4516 0.5205 17 R 0.0439 0.3353 0.6208 18 P 0.0502 0.2560 0.6937 19 K 0.0365 0.3723 0.5912 20 D 0.0308 0.5843 0.3849 21 E 0.0188 0.8335 0.1477 22 F 0.0190 0.8674 0.1136 23 I 0.0265 0.8740 0.0995 24 R 0.0220 0.8739 0.1041 25 D 0.0328 0.8113 0.1558 26 S 0.0399 0.7341 0.2260 27 A 0.0840 0.7487 0.1673 28 I 0.1195 0.7333 0.1472 29 Q 0.1634 0.6788 0.1579 30 R 0.1813 0.6673 0.1514 31 F 0.1973 0.6752 0.1276 32 E 0.1452 0.7681 0.0867 33 F 0.1401 0.7870 0.0730 34 T 0.0660 0.8754 0.0586 35 F 0.0561 0.8857 0.0583 36 E 0.0227 0.9236 0.0536 37 L 0.0133 0.9201 0.0667 38 A 0.0060 0.9359 0.0581 39 W 0.0051 0.9510 0.0439 40 K 0.0050 0.9529 0.0421 41 T 0.0048 0.9545 0.0407 42 L 0.0047 0.9549 0.0403 43 K 0.0047 0.9548 0.0404 44 T 0.0048 0.9508 0.0444 45 F 0.0049 0.9408 0.0543 46 L 0.0072 0.9145 0.0782 47 E 0.0075 0.8784 0.1141 48 L 0.0166 0.7857 0.1978 49 Q 0.0424 0.4501 0.5075 50 G 0.0328 0.0757 0.8915 51 L 0.0754 0.0555 0.8692 52 E 0.1123 0.0597 0.8280 53 A 0.1707 0.0715 0.7578 54 R 0.1339 0.0625 0.8035 55 S 0.1110 0.0374 0.8516 56 P 0.0268 0.6742 0.2990 57 R 0.0066 0.9188 0.0747 58 A 0.0052 0.9466 0.0482 59 A 0.0048 0.9544 0.0408 60 I 0.0047 0.9565 0.0387 61 R 0.0047 0.9563 0.0389 62 G 0.0049 0.9531 0.0421 63 A 0.0049 0.9472 0.0479 64 F 0.0061 0.9237 0.0702 65 Q 0.0064 0.8585 0.1351 66 V 0.0430 0.4655 0.4915 67 G 0.0409 0.1624 0.7967 68 L 0.0885 0.1290 0.7824 69 L 0.1399 0.0944 0.7657 70 P 0.0597 0.0910 0.8493 71 E 0.0706 0.1222 0.8072 72 D 0.0403 0.5842 0.3755 73 P 0.0517 0.7573 0.1910 74 F 0.0685 0.8151 0.1164 75 W 0.0743 0.8533 0.0725 76 L 0.0500 0.8928 0.0573 77 E 0.0592 0.8788 0.0620 78 M 0.0536 0.8602 0.0862 79 L 0.0831 0.7931 0.1238 80 E 0.0608 0.7075 0.2317 81 L 0.0387 0.5901 0.3712 82 R 0.0621 0.4023 0.5356 83 N 0.0989 0.1927 0.7084 84 L 0.0841 0.2085 0.7073 85 T 0.1648 0.2176 0.6176 86 N 0.2165 0.2110 0.5724 87 H 0.2369 0.1745 0.5886 88 T 0.2515 0.1489 0.5996 89 Y 0.1335 0.1529 0.7136 90 D 0.0702 0.1652 0.7646 91 E 0.0058 0.9233 0.0709 92 A 0.0051 0.9389 0.0560 93 L 0.0050 0.9440 0.0510 94 A 0.0048 0.9513 0.0439 95 E 0.0048 0.9522 0.0431 96 R 0.0048 0.9528 0.0425 97 I 0.0048 0.9502 0.0451 98 Y 0.0048 0.9422 0.0530 99 A 0.0050 0.8961 0.0989 100 E 0.0062 0.8417 0.1521 101 L 0.0070 0.8483 0.1448 102 P 0.0055 0.8861 0.1084 103 K 0.0057 0.8626 0.1318 104 A 0.0061 0.8691 0.1248 105 L 0.0059 0.9010 0.0931 106 E 0.0054 0.9038 0.0909 107 R 0.0052 0.9218 0.0730 108 F 0.0050 0.9399 0.0551 109 Q 0.0050 0.9445 0.0506 110 E 0.0049 0.9496 0.0455 111 L 0.0050 0.9469 0.0481 112 L 0.0057 0.9382 0.0561 113 R 0.0058 0.9118 0.0824 114 R 0.0080 0.8844 0.1075 115 L 0.0225 0.7877 0.1898 116 E 0.0215 0.6568 0.3217 117 E 0.0394 0.4006 0.5600 118 P 0.0396 0.1201 0.8403 119 A 0.0366 0.0511 0.9124