# This file is the result of combining several RDB files, specifically # T0340.t06.dssp-ebghstl.rdb (weight 1.53986) # T0340.t06.stride-ebghtl.rdb (weight 1.24869) # T0340.t06.str2.rdb (weight 1.54758) # T0340.t06.alpha.rdb (weight 0.659012) # T0340.t04.dssp-ebghstl.rdb (weight 1.53986) # T0340.t04.stride-ebghtl.rdb (weight 1.24869) # T0340.t04.str2.rdb (weight 1.54758) # T0340.t04.alpha.rdb (weight 0.659012) # T0340.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0340.t2k.stride-ebghtl.rdb (weight 1.24869) # T0340.t2k.str2.rdb (weight 1.54758) # T0340.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 T0340.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.stride-ebghtl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.str2.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.alpha.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.stride-ebghtl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.str2.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t04.alpha.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1647.22 # # ============================================ # Comments from T0340.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1980 # # ============================================ # Comments from T0340.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1980 # # ============================================ # Comments from T0340.t2k.str2.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1980 # # ============================================ # Comments from T0340.t2k.alpha.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1980 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0729 0.0675 0.8596 2 M 0.1057 0.0715 0.8229 3 L 0.1427 0.0476 0.8097 4 R 0.1880 0.0222 0.7898 5 P 0.3864 0.0244 0.5892 6 R 0.6748 0.0342 0.2910 7 L 0.8616 0.0137 0.1246 8 C 0.8691 0.0157 0.1153 9 H 0.8915 0.0102 0.0983 10 L 0.8461 0.0122 0.1416 11 R 0.7242 0.0243 0.2515 12 K 0.3908 0.0366 0.5725 13 G 0.1128 0.0463 0.8409 14 P 0.1054 0.0650 0.8296 15 Q 0.1787 0.0572 0.7641 16 G 0.3835 0.0514 0.5651 17 Y 0.5870 0.0305 0.3826 18 G 0.7567 0.0212 0.2221 19 F 0.8380 0.0136 0.1484 20 N 0.8498 0.0122 0.1380 21 L 0.8374 0.0175 0.1450 22 H 0.7502 0.0264 0.2234 23 S 0.5214 0.0487 0.4299 24 D 0.2849 0.0673 0.6479 25 K 0.1791 0.1002 0.7207 26 S 0.1442 0.0926 0.7631 27 R 0.1554 0.0617 0.7829 28 P 0.1977 0.0514 0.7509 29 G 0.4940 0.0232 0.4828 30 Q 0.8326 0.0051 0.1622 31 Y 0.9041 0.0042 0.0917 32 I 0.9075 0.0035 0.0889 33 R 0.8388 0.0259 0.1353 34 S 0.8081 0.0071 0.1848 35 V 0.6661 0.0134 0.3205 36 D 0.2268 0.0196 0.7536 37 P 0.0368 0.0709 0.8923 38 G 0.0258 0.0460 0.9283 39 S 0.0644 0.1058 0.8298 40 P 0.0336 0.7793 0.1871 41 A 0.0116 0.8651 0.1233 42 A 0.0106 0.8643 0.1252 43 R 0.0208 0.8138 0.1654 44 S 0.0415 0.3842 0.5743 45 G 0.0304 0.0559 0.9136 46 L 0.1040 0.0131 0.8829 47 R 0.1070 0.0200 0.8730 48 A 0.0360 0.2024 0.7616 49 Q 0.0541 0.1161 0.8298 50 D 0.3689 0.0662 0.5649 51 R 0.8259 0.0119 0.1622 52 L 0.8960 0.0074 0.0966 53 I 0.9078 0.0065 0.0857 54 E 0.8928 0.0093 0.0979 55 V 0.8074 0.0179 0.1747 56 N 0.1338 0.0270 0.8392 57 G 0.0526 0.0529 0.8945 58 Q 0.5769 0.0222 0.4009 59 N 0.5973 0.0207 0.3819 60 V 0.4692 0.0703 0.4605 61 E 0.2538 0.1051 0.6411 62 G 0.1145 0.0863 0.7992 63 L 0.1999 0.0352 0.7649 64 R 0.1715 0.0363 0.7923 65 H 0.0058 0.9111 0.0831 66 A 0.0047 0.9522 0.0430 67 E 0.0049 0.9570 0.0381 68 V 0.0047 0.9585 0.0368 69 V 0.0047 0.9580 0.0373 70 A 0.0047 0.9547 0.0405 71 S 0.0050 0.9474 0.0476 72 I 0.0091 0.9236 0.0673 73 K 0.0127 0.8278 0.1595 74 A 0.0336 0.4467 0.5196 75 R 0.0615 0.1004 0.8380 76 E 0.0408 0.0762 0.8830 77 D 0.0483 0.0522 0.8996 78 E 0.3366 0.0152 0.6482 79 A 0.7940 0.0038 0.2021 80 R 0.9063 0.0037 0.0900 81 L 0.9226 0.0032 0.0741 82 L 0.9190 0.0034 0.0775 83 V 0.9029 0.0035 0.0936 84 V 0.7880 0.0053 0.2066 85 G 0.4301 0.0119 0.5580 86 P 0.1169 0.0367 0.8465 87 S 0.0432 0.1208 0.8360 88 T 0.0431 0.1263 0.8306 89 R 0.0574 0.0980 0.8446 90 L 0.0410 0.0427 0.9163