# This file is the result of combining several RDB files, specifically # T0314.t06.dssp-ebghstl.rdb (weight 1.53986) # T0314.t06.stride-ebghtl.rdb (weight 1.24869) # T0314.t06.str2.rdb (weight 1.54758) # T0314.t06.alpha.rdb (weight 0.659012) # T0314.t04.dssp-ebghstl.rdb (weight 1.53986) # T0314.t04.stride-ebghtl.rdb (weight 1.24869) # T0314.t04.str2.rdb (weight 1.54758) # T0314.t04.alpha.rdb (weight 0.659012) # T0314.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0314.t2k.stride-ebghtl.rdb (weight 1.24869) # T0314.t2k.str2.rdb (weight 1.54758) # T0314.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 T0314.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.t06-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 2.50627 # # ============================================ # Comments from T0314.t06.stride-ebghtl.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.t06-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 2.50627 # # ============================================ # Comments from T0314.t06.str2.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.t06-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 2.50627 # # ============================================ # Comments from T0314.t06.alpha.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.t06-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 2.50627 # # ============================================ # Comments from T0314.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.stride-ebghtl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.str2.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t04.alpha.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 5 # # ============================================ # Comments from T0314.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 5 # # ============================================ # Comments from T0314.t2k.str2.rdb # ============================================ # TARGET T0314 # Using neural net t06-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 T0314.t2k-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 2.48375 # # ============================================ # Comments from T0314.t2k.alpha.rdb # ============================================ # TARGET T0314 # 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 T0314.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0925 0.0317 0.8758 2 S 0.2561 0.0601 0.6838 3 I 0.2982 0.0940 0.6078 4 T 0.2211 0.1182 0.6608 5 S 0.0719 0.5864 0.3416 6 T 0.0227 0.7764 0.2009 7 D 0.0186 0.8147 0.1666 8 I 0.0131 0.8713 0.1157 9 C 0.0104 0.8694 0.1203 10 Q 0.0106 0.8494 0.1400 11 A 0.0074 0.8789 0.1136 12 A 0.0090 0.8774 0.1136 13 D 0.0081 0.7990 0.1929 14 A 0.0144 0.7040 0.2816 15 L 0.0657 0.4234 0.5109 16 K 0.0523 0.2544 0.6933 17 G 0.1662 0.1746 0.6592 18 F 0.4150 0.1296 0.4554 19 V 0.5856 0.0767 0.3377 20 G 0.5180 0.0710 0.4110 21 F 0.4408 0.0662 0.4930 22 N 0.3242 0.0716 0.6043 23 R 0.1308 0.1232 0.7460 24 K 0.1459 0.1208 0.7334 25 T 0.1665 0.0566 0.7769 26 G 0.1816 0.0297 0.7887 27 R 0.5574 0.0121 0.4305 28 Y 0.8802 0.0037 0.1162 29 I 0.9059 0.0042 0.0899 30 V 0.9025 0.0044 0.0930 31 R 0.8525 0.0069 0.1406 32 F 0.6092 0.0200 0.3708 33 S 0.3353 0.0305 0.6343 34 E 0.1404 0.1870 0.6726 35 D 0.0692 0.2551 0.6757 36 S 0.0681 0.3180 0.6139 37 F 0.0734 0.2344 0.6923 38 G 0.0871 0.1266 0.7863 39 M 0.1602 0.1089 0.7309 40 D 0.2462 0.1623 0.5915 41 V 0.2138 0.3333 0.4529 42 A 0.2007 0.3234 0.4759 43 D 0.1130 0.3669 0.5201 44 D 0.0701 0.3025 0.6275 45 S 0.1032 0.1805 0.7163 46 I 0.2571 0.0909 0.6520 47 T 0.2295 0.0394 0.7311 48 P 0.1959 0.0827 0.7214 49 T 0.1455 0.2229 0.6316 50 S 0.1506 0.2909 0.5585 51 E 0.2624 0.2801 0.4575 52 F 0.4936 0.1406 0.3658 53 V 0.6044 0.0715 0.3241 54 W 0.5925 0.0404 0.3670 55 S 0.4317 0.0320 0.5363 56 S 0.2945 0.0688 0.6367 57 V 0.1399 0.1700 0.6901 58 R 0.0981 0.2234 0.6785 59 D 0.0721 0.3288 0.5991 60 D 0.1627 0.3756 0.4617 61 V 0.3237 0.3791 0.2972 62 M 0.3693 0.3719 0.2588 63 R 0.3319 0.4270 0.2411 64 L 0.1793 0.4994 0.3214 65 G 0.1032 0.5842 0.3126 66 R 0.0266 0.8423 0.1311 67 E 0.0237 0.8935 0.0828 68 Q 0.0138 0.9280 0.0581 69 L 0.0106 0.9441 0.0453 70 Q 0.0075 0.9473 0.0452 71 I 0.0082 0.9406 0.0512 72 L 0.0091 0.9245 0.0664 73 L 0.0119 0.8317 0.1564 74 E 0.0151 0.6654 0.3194 75 Q 0.0575 0.4441 0.4984 76 N 0.1087 0.2226 0.6687 77 I 0.0648 0.2510 0.6842 78 N 0.0841 0.2394 0.6765 79 E 0.0608 0.4209 0.5183 80 R 0.1188 0.3127 0.5685 81 L 0.2298 0.1816 0.5886 82 N 0.1975 0.1064 0.6960 83 I 0.0719 0.2081 0.7200 84 G 0.0488 0.1872 0.7640 85 E 0.1026 0.2152 0.6823 86 P 0.1917 0.3457 0.4626 87 L 0.2568 0.4542 0.2890 88 L 0.4197 0.4335 0.1468 89 V 0.5156 0.3595 0.1249 90 Y 0.5242 0.3354 0.1404 91 L 0.5315 0.2690 0.1996 92 R 0.4078 0.1897 0.4024 93 R 0.1474 0.3196 0.5331 94 Q 0.0538 0.2730 0.6731 95 D 0.0456 0.2190 0.7354 96 L 0.0742 0.0828 0.8429 97 P 0.0541 0.1594 0.7865 98 E 0.1966 0.4041 0.3993 99 I 0.3188 0.4821 0.1991 100 T 0.3472 0.4685 0.1842 101 A 0.3389 0.4696 0.1915 102 Q 0.2869 0.4962 0.2169 103 R 0.2053 0.4703 0.3243 104 Q 0.1402 0.3930 0.4668 105 L 0.0984 0.1985 0.7031 106 R 0.0407 0.0523 0.9070