# 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 321 # # ============================================ # 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 321 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 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 321 # # ============================================ # 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 321 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1391 0.0643 0.7965 2 S 0.1533 0.0670 0.7797 3 D 0.1171 0.0902 0.7927 4 N 0.0669 0.0954 0.8377 5 S 0.0357 0.1417 0.8226 6 K 0.0675 0.0484 0.8841 7 T 0.1749 0.0161 0.8090 8 R 0.6521 0.0044 0.3435 9 V 0.9221 0.0032 0.0747 10 V 0.9309 0.0032 0.0659 11 V 0.9281 0.0034 0.0686 12 G 0.9043 0.0041 0.0915 13 M 0.7178 0.0226 0.2597 14 S 0.2730 0.0313 0.6957 15 G 0.1233 0.0677 0.8090 16 G 0.0606 0.1785 0.7609 17 V 0.0454 0.5909 0.3636 18 D 0.0168 0.7729 0.2103 19 S 0.0051 0.9126 0.0823 20 S 0.0048 0.9546 0.0406 21 V 0.0047 0.9596 0.0357 22 T 0.0047 0.9598 0.0356 23 A 0.0047 0.9601 0.0352 24 L 0.0047 0.9608 0.0345 25 L 0.0047 0.9602 0.0352 26 L 0.0047 0.9588 0.0365 27 K 0.0049 0.9509 0.0442 28 E 0.0056 0.9074 0.0869 29 Q 0.0406 0.4475 0.5119 30 G 0.0385 0.0332 0.9283 31 Y 0.1131 0.0176 0.8694 32 D 0.5397 0.0138 0.4465 33 V 0.7994 0.0054 0.1952 34 I 0.8344 0.0309 0.1347 35 G 0.9069 0.0071 0.0860 36 I 0.9189 0.0049 0.0762 37 F 0.9090 0.0053 0.0857 38 M 0.8738 0.0103 0.1159 39 K 0.7877 0.0259 0.1864 40 N 0.6526 0.0307 0.3167 41 W 0.4066 0.0541 0.5393 42 D 0.2644 0.0599 0.6758 43 D 0.1482 0.0939 0.7579 44 T 0.0813 0.1019 0.8168 45 D 0.0634 0.1059 0.8307 46 E 0.0670 0.1035 0.8295 47 N 0.0918 0.1161 0.7921 48 G 0.1198 0.1037 0.7765 49 V 0.2089 0.1073 0.6839 50 C 0.2572 0.0844 0.6583 51 T 0.1537 0.1035 0.7428 52 A 0.0875 0.2092 0.7033 53 T 0.0250 0.6625 0.3125 54 E 0.0245 0.6149 0.3606 55 D 0.0358 0.6145 0.3497 56 Y 0.0053 0.9362 0.0584 57 K 0.0049 0.9512 0.0439 58 D 0.0048 0.9559 0.0393 59 V 0.0047 0.9590 0.0362 60 V 0.0047 0.9603 0.0350 61 A 0.0047 0.9602 0.0351 62 V 0.0047 0.9590 0.0363 63 A 0.0047 0.9577 0.0375 64 D 0.0053 0.9452 0.0495 65 Q 0.0068 0.9080 0.0852 66 I 0.0471 0.4746 0.4782 67 G 0.0502 0.0147 0.9351 68 I 0.0700 0.0082 0.9217 69 P 0.1818 0.0128 0.8053 70 Y 0.6225 0.0090 0.3685 71 Y 0.8399 0.0065 0.1535 72 S 0.9104 0.0047 0.0849 73 V 0.8674 0.0105 0.1221 74 N 0.6245 0.0111 0.3643 75 F 0.0286 0.6270 0.3445 76 E 0.0088 0.7427 0.2485 77 K 0.0068 0.8877 0.1055 78 E 0.0073 0.9060 0.0867 79 Y 0.0097 0.8827 0.1076 80 W 0.0064 0.9067 0.0869 81 D 0.0076 0.8987 0.0938 82 R 0.0087 0.8371 0.1542 83 V 0.0142 0.8420 0.1439 84 F 0.0074 0.8928 0.0997 85 E 0.0054 0.9446 0.0501 86 Y 0.0047 0.9513 0.0440 87 F 0.0048 0.9532 0.0420 88 L 0.0048 0.9534 0.0418 89 A 0.0048 0.9540 0.0412 90 E 0.0055 0.9459 0.0486 91 Y 0.0085 0.9228 0.0686 92 R 0.0086 0.8648 0.1266 93 A 0.0337 0.5228 0.4435 94 G 0.0298 0.1604 0.8098 95 R 0.0723 0.0443 0.8834 96 T 0.0952 0.0244 0.8804 97 P 0.0671 0.0415 0.8913 98 N 0.0880 0.0396 0.8724 99 P 0.1147 0.1157 0.7696 100 D 0.2340 0.1491 0.6168 101 V 0.2433 0.2831 0.4736 102 M 0.1956 0.2652 0.5392 103 C 0.0960 0.2948 0.6093 104 N 0.0824 0.2366 0.6809 105 K 0.0729 0.4682 0.4589 106 E 0.1784 0.4944 0.3272 107 I 0.3262 0.3868 0.2870 108 K 0.2816 0.3630 0.3554 109 F 0.0298 0.8075 0.1628 110 K 0.0069 0.9248 0.0683 111 A 0.0059 0.9421 0.0521 112 F 0.0053 0.9483 0.0464 113 L 0.0055 0.9545 0.0400 114 D 0.0051 0.9526 0.0423 115 Y 0.0050 0.9509 0.0441 116 A 0.0051 0.9496 0.0453 117 I 0.0051 0.9411 0.0538 118 T 0.0061 0.8713 0.1226 119 L 0.0442 0.3848 0.5710 120 G 0.0480 0.0195 0.9325 121 A 0.0922 0.0098 0.8980 122 D 0.1930 0.0530 0.7540 123 Y 0.8862 0.0125 0.1013 124 V 0.9126 0.0072 0.0803 125 A 0.8842 0.0090 0.1068 126 T 0.7307 0.0195 0.2498 127 G 0.2594 0.0276 0.7130 128 H 0.2634 0.0641 0.6725 129 Y 0.5761 0.0652 0.3587 130 A 0.7656 0.0364 0.1981 131 R 0.8057 0.0308 0.1635 132 V 0.8020 0.0285 0.1696 133 A 0.6856 0.0453 0.2690 134 R 0.5338 0.0544 0.4118 135 D 0.2751 0.0561 0.6688 136 E 0.1093 0.0623 0.8284 137 D 0.0661 0.0271 0.9068