# This file is the result of combining several RDB files, specifically # T0396.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0396.t2k.stride-ebghtl.rdb (weight 1.24869) # T0396.t2k.str.rdb (weight 1.53983) # 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 T0396.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0396 # 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 T0396.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 141 # # ============================================ # Comments from T0396.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0396 # 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 T0396.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 141 # # ============================================ # Comments from T0396.t2k.str.rdb # ============================================ # TARGET T0396 # 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 T0396.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 141 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0254 0.0239 0.9507 2 S 0.0568 0.0302 0.9130 3 M 0.0108 0.6459 0.3432 4 L 0.0078 0.6701 0.3221 5 H 0.0107 0.7371 0.2521 6 W 0.0203 0.6376 0.3421 7 G 0.0111 0.6329 0.3559 8 P 0.0038 0.9508 0.0454 9 K 0.0037 0.9698 0.0264 10 Y 0.0037 0.9716 0.0247 11 W 0.0037 0.9745 0.0218 12 R 0.0037 0.9737 0.0225 13 S 0.0037 0.9724 0.0239 14 L 0.0041 0.9713 0.0246 15 H 0.0041 0.9700 0.0259 16 L 0.0038 0.9656 0.0306 17 Y 0.0039 0.9557 0.0404 18 A 0.0075 0.9174 0.0751 19 I 0.0146 0.7927 0.1926 20 F 0.0297 0.5751 0.3952 21 F 0.0404 0.1189 0.8408 22 S 0.0313 0.0588 0.9099 23 D 0.0233 0.0584 0.9183 24 A 0.0191 0.0310 0.9499 25 P 0.0166 0.0267 0.9567 26 S 0.0158 0.0229 0.9613 27 W 0.0049 0.8385 0.1566 28 K 0.0040 0.8943 0.1017 29 E 0.0038 0.9349 0.0613 30 K 0.0037 0.9649 0.0313 31 Y 0.0037 0.9634 0.0328 32 E 0.0037 0.9608 0.0354 33 A 0.0037 0.9712 0.0251 34 I 0.0037 0.9743 0.0220 35 Q 0.0037 0.9700 0.0262 36 W 0.0037 0.9693 0.0269 37 I 0.0040 0.9680 0.0280 38 L 0.0038 0.9557 0.0405 39 N 0.0038 0.9248 0.0713 40 F 0.0048 0.9000 0.0952 41 I 0.0053 0.8251 0.1696 42 E 0.0067 0.7133 0.2801 43 S 0.0130 0.6443 0.3426 44 L 0.0748 0.2041 0.7211 45 P 0.0341 0.1217 0.8441 46 C 0.0197 0.2684 0.7119 47 T 0.0039 0.8748 0.1214 48 R 0.0038 0.9076 0.0886 49 C 0.0041 0.9255 0.0703 50 Q 0.0037 0.9617 0.0345 51 H 0.0037 0.9575 0.0388 52 H 0.0037 0.9546 0.0417 53 A 0.0037 0.9681 0.0282 54 F 0.0037 0.9741 0.0222 55 S 0.0037 0.9707 0.0256 56 Y 0.0037 0.9668 0.0295 57 L 0.0038 0.9533 0.0430 58 T 0.0039 0.8658 0.1303 59 K 0.0054 0.6874 0.3072 60 N 0.0186 0.2238 0.7576 61 P 0.0236 0.0379 0.9384 62 L 0.0355 0.0440 0.9204 63 T 0.0953 0.0621 0.8426 64 L 0.1511 0.0413 0.8076 65 N 0.0983 0.0272 0.8745 66 N 0.0558 0.0413 0.9029 67 S 0.0043 0.8937 0.1020 68 E 0.0038 0.9412 0.0550 69 D 0.0038 0.9634 0.0329 70 F 0.0037 0.9730 0.0232 71 Q 0.0037 0.9745 0.0218 72 Y 0.0037 0.9752 0.0211 73 W 0.0037 0.9738 0.0225 74 T 0.0037 0.9716 0.0246 75 F 0.0037 0.9664 0.0299 76 A 0.0037 0.9471 0.0492 77 F 0.0038 0.9072 0.0891 78 H 0.0045 0.8444 0.1510 79 N 0.0044 0.8542 0.1414 80 N 0.0066 0.9108 0.0826 81 V 0.0037 0.9550 0.0413 82 N 0.0041 0.9499 0.0460 83 N 0.0048 0.9397 0.0554 84 R 0.0049 0.9025 0.0927 85 L 0.0069 0.5643 0.4288 86 N 0.0112 0.0742 0.9146 87 K 0.0239 0.0314 0.9448 88 K 0.0786 0.0578 0.8636 89 I 0.1154 0.1394 0.7453 90 I 0.1504 0.1067 0.7429 91 S 0.1184 0.0935 0.7882 92 W 0.0396 0.3815 0.5790 93 S 0.0173 0.5708 0.4119 94 E 0.0212 0.6042 0.3747 95 Y 0.0379 0.5917 0.3704 96 K 0.0452 0.6241 0.3307 97 N 0.0620 0.6883 0.2498 98 I 0.0611 0.7125 0.2263 99 Y 0.0794 0.6286 0.2921 100 E 0.0730 0.4739 0.4531 101 Q 0.0419 0.2986 0.6596 102 S 0.0370 0.1253 0.8377 103 I 0.0501 0.0882 0.8617 104 L 0.0416 0.0645 0.8939 105 K 0.0102 0.0072 0.9827