# This file is the result of combining several RDB files, specifically # T0492.t04.dssp-ebghstl.rdb (weight 1.53986) # T0492.t04.stride-ebghtl.rdb (weight 1.24869) # T0492.t04.str2.rdb (weight 1.54758) # T0492.t04.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 T0492.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0492 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0492.t04-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 61.0306 # # ============================================ # Comments from T0492.t04.stride-ebghtl.rdb # ============================================ # TARGET T0492 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0492.t04-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 61.0306 # # ============================================ # Comments from T0492.t04.str2.rdb # ============================================ # TARGET T0492 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0492.t04-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 61.0306 # # ============================================ # Comments from T0492.t04.alpha.rdb # ============================================ # TARGET T0492 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0492.t04-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 61.0306 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1744 0.0377 0.7879 2 F 0.3311 0.0179 0.6510 3 S 0.3068 0.0200 0.6732 4 L 0.0414 0.7317 0.2269 5 R 0.0406 0.6904 0.2689 6 D 0.0583 0.5582 0.3835 7 A 0.1332 0.0753 0.7915 8 K 0.0836 0.0494 0.8669 9 C 0.0354 0.0872 0.8773 10 G 0.0453 0.0451 0.9096 11 Q 0.3429 0.0165 0.6406 12 T 0.7775 0.0040 0.2185 13 V 0.8630 0.0045 0.1326 14 K 0.9178 0.0040 0.0782 15 V 0.9211 0.0030 0.0759 16 V 0.8613 0.0226 0.1161 17 K 0.8868 0.0038 0.1094 18 L 0.8079 0.0075 0.1846 19 H 0.4490 0.0240 0.5270 20 G 0.1301 0.0352 0.8346 21 T 0.0632 0.1098 0.8270 22 G 0.0235 0.5191 0.4574 23 A 0.0158 0.8464 0.1378 24 L 0.0125 0.9248 0.0628 25 K 0.0105 0.9400 0.0495 26 R 0.0075 0.9493 0.0431 27 R 0.0084 0.9491 0.0425 28 I 0.0115 0.9448 0.0437 29 M 0.0157 0.9309 0.0534 30 D 0.0133 0.9184 0.0683 31 M 0.0488 0.5608 0.3904 32 G 0.0543 0.0670 0.8787 33 I 0.1373 0.0297 0.8329 34 T 0.1238 0.0324 0.8438 35 R 0.0333 0.0660 0.9006 36 G 0.0353 0.0351 0.9297 37 C 0.3157 0.0117 0.6726 38 E 0.7863 0.0039 0.2098 39 I 0.8991 0.0037 0.0971 40 Y 0.9232 0.0037 0.0731 41 I 0.9162 0.0031 0.0808 42 R 0.8742 0.0098 0.1160 43 K 0.8345 0.0044 0.1611 44 V 0.7063 0.0108 0.2830 45 A 0.3015 0.0161 0.6824 46 P 0.1426 0.0552 0.8022 47 L 0.0969 0.0446 0.8586 48 G 0.0847 0.0382 0.8771 49 D 0.1453 0.0146 0.8401 50 P 0.3091 0.0182 0.6727 51 I 0.7717 0.0100 0.2183 52 Q 0.9110 0.0037 0.0853 53 I 0.9250 0.0035 0.0715 54 N 0.9179 0.0037 0.0784 55 V 0.8198 0.0099 0.1703 56 R 0.2415 0.0392 0.7193 57 G 0.1173 0.0289 0.8538 58 Y 0.6813 0.0297 0.2891 59 E 0.8692 0.0219 0.1089 60 L 0.8710 0.0325 0.0965 61 S 0.8567 0.0373 0.1060 62 L 0.7372 0.0559 0.2069 63 R 0.4372 0.1014 0.4614 64 K 0.0657 0.6287 0.3057 65 S 0.0351 0.6759 0.2890 66 A 0.0283 0.6916 0.2801 67 A 0.1309 0.5502 0.3189 68 E 0.1008 0.4331 0.4662 69 M 0.3611 0.3142 0.3247 70 I 0.5671 0.1779 0.2550 71 E 0.6478 0.0823 0.2699 72 V 0.4946 0.0300 0.4754 73 E 0.2050 0.0266 0.7684