# 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) # T0492.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0492.t2k.stride-ebghtl.rdb (weight 1.24869) # T0492.t2k.str2.rdb (weight 1.54758) # T0492.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 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 # # ============================================ # 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 347 # # ============================================ # 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 347 # # ============================================ # Comments from T0492.t2k.str2.rdb # ============================================ # TARGET T0492 # 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 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 347 # # ============================================ # Comments from T0492.t2k.alpha.rdb # ============================================ # TARGET T0492 # 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 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 347 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0563 0.0394 0.9042 2 F 0.1779 0.0384 0.7838 3 S 0.2066 0.0660 0.7274 4 L 0.0446 0.6711 0.2843 5 R 0.0365 0.6885 0.2749 6 D 0.0655 0.6245 0.3100 7 A 0.2296 0.0676 0.7028 8 K 0.0829 0.0224 0.8947 9 C 0.0355 0.0953 0.8692 10 G 0.0280 0.0517 0.9203 11 Q 0.2840 0.0177 0.6984 12 T 0.8100 0.0045 0.1855 13 V 0.8901 0.0047 0.1052 14 K 0.9086 0.0047 0.0867 15 V 0.9118 0.0033 0.0850 16 V 0.8600 0.0186 0.1215 17 K 0.8602 0.0043 0.1355 18 L 0.7317 0.0088 0.2596 19 H 0.3861 0.0175 0.5963 20 G 0.1008 0.0416 0.8576 21 T 0.0428 0.1287 0.8285 22 G 0.0264 0.5749 0.3987 23 A 0.0138 0.8577 0.1285 24 L 0.0096 0.9279 0.0625 25 K 0.0060 0.9508 0.0432 26 R 0.0071 0.9516 0.0412 27 R 0.0055 0.9538 0.0407 28 I 0.0057 0.9509 0.0434 29 M 0.0056 0.9318 0.0626 30 D 0.0062 0.8794 0.1144 31 M 0.0417 0.4742 0.4841 32 G 0.0423 0.0636 0.8940 33 I 0.1552 0.0249 0.8199 34 T 0.1312 0.0173 0.8515 35 R 0.0477 0.0660 0.8864 36 G 0.0399 0.0456 0.9145 37 C 0.4013 0.0127 0.5860 38 E 0.8578 0.0034 0.1388 39 I 0.9056 0.0038 0.0907 40 Y 0.9173 0.0037 0.0790 41 I 0.9141 0.0034 0.0826 42 R 0.8976 0.0098 0.0927 43 K 0.8850 0.0051 0.1099 44 V 0.7564 0.0125 0.2311 45 A 0.4673 0.0126 0.5201 46 P 0.2028 0.0386 0.7586 47 L 0.0735 0.0453 0.8812 48 G 0.0658 0.0330 0.9012 49 D 0.1301 0.0188 0.8511 50 P 0.4486 0.0155 0.5358 51 I 0.8719 0.0052 0.1229 52 Q 0.9249 0.0032 0.0719 53 I 0.9265 0.0034 0.0701 54 N 0.9263 0.0032 0.0706 55 V 0.8717 0.0119 0.1165 56 R 0.2638 0.0312 0.7049 57 G 0.0927 0.0667 0.8407 58 Y 0.7019 0.0363 0.2618 59 E 0.8820 0.0174 0.1005 60 L 0.8975 0.0086 0.0939 61 S 0.8875 0.0104 0.1020 62 L 0.7549 0.0249 0.2202 63 R 0.4401 0.0407 0.5192 64 K 0.0701 0.6605 0.2694 65 S 0.0436 0.7141 0.2423 66 A 0.0444 0.7280 0.2276 67 A 0.0894 0.6636 0.2470 68 E 0.1155 0.5223 0.3622 69 M 0.2016 0.3773 0.4210 70 I 0.4178 0.1517 0.4305 71 E 0.6075 0.0809 0.3116 72 V 0.3837 0.0596 0.5567 73 E 0.0556 0.0318 0.9126