# This file is the result of combining several RDB files, specifically # T0492.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0492.t2k.stride-ebghtl.rdb (weight 1.24869) # T0492.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 T0492.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0492 # 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 T0492.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 342 # # ============================================ # Comments from T0492.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0492 # 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 T0492.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 342 # # ============================================ # Comments from T0492.t2k.str.rdb # ============================================ # TARGET T0492 # 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 T0492.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 342 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0175 0.0067 0.9758 2 F 0.2100 0.0154 0.7746 3 S 0.2304 0.0364 0.7332 4 L 0.0312 0.7847 0.1841 5 R 0.0270 0.7451 0.2279 6 D 0.0248 0.7431 0.2321 7 A 0.0729 0.1023 0.8248 8 K 0.0335 0.0307 0.9358 9 C 0.0194 0.0740 0.9066 10 G 0.0162 0.0463 0.9375 11 Q 0.2460 0.0173 0.7367 12 T 0.7856 0.0027 0.2116 13 V 0.9406 0.0024 0.0570 14 K 0.9718 0.0024 0.0257 15 V 0.9618 0.0028 0.0354 16 V 0.9598 0.0025 0.0377 17 K 0.9372 0.0029 0.0599 18 L 0.8312 0.0038 0.1650 19 H 0.5101 0.0108 0.4791 20 G 0.0987 0.0504 0.8509 21 T 0.0246 0.1258 0.8496 22 G 0.0075 0.5957 0.3968 23 A 0.0082 0.8678 0.1240 24 L 0.0062 0.9415 0.0522 25 K 0.0048 0.9633 0.0319 26 R 0.0055 0.9612 0.0332 27 R 0.0040 0.9681 0.0278 28 I 0.0044 0.9671 0.0285 29 M 0.0038 0.9583 0.0379 30 D 0.0049 0.9095 0.0857 31 M 0.0058 0.5584 0.4358 32 G 0.0169 0.0386 0.9445 33 I 0.1037 0.0156 0.8807 34 T 0.1049 0.0180 0.8771 35 R 0.0328 0.0388 0.9284 36 G 0.0278 0.0203 0.9519 37 C 0.4034 0.0077 0.5889 38 E 0.8942 0.0024 0.1034 39 I 0.9624 0.0024 0.0353 40 Y 0.9739 0.0024 0.0237 41 I 0.9738 0.0027 0.0235 42 R 0.9659 0.0025 0.0316 43 K 0.9482 0.0026 0.0492 44 V 0.8107 0.0034 0.1859 45 A 0.4490 0.0093 0.5417 46 P 0.1382 0.0322 0.8296 47 L 0.0645 0.0396 0.8960 48 G 0.0428 0.0230 0.9342 49 D 0.1106 0.0125 0.8769 50 P 0.3376 0.0094 0.6530 51 I 0.8837 0.0036 0.1126 52 Q 0.9679 0.0024 0.0297 53 I 0.9747 0.0024 0.0229 54 N 0.9744 0.0024 0.0232 55 V 0.9485 0.0026 0.0489 56 R 0.2440 0.0204 0.7356 57 G 0.0734 0.0482 0.8784 58 Y 0.7149 0.0368 0.2483 59 E 0.9002 0.0204 0.0793 60 L 0.9305 0.0114 0.0580 61 S 0.9177 0.0131 0.0692 62 L 0.8484 0.0191 0.1325 63 R 0.4788 0.0566 0.4646 64 K 0.0723 0.6816 0.2461 65 S 0.0455 0.7022 0.2523 66 A 0.0519 0.7389 0.2092 67 A 0.0848 0.6802 0.2350 68 E 0.1438 0.4857 0.3705 69 M 0.2485 0.3341 0.4174 70 I 0.5068 0.1409 0.3523 71 E 0.6200 0.1099 0.2700 72 V 0.4246 0.0685 0.5069 73 E 0.0258 0.0051 0.9691