# This file is the result of combining several RDB files, specifically # T0538.t04.dssp-ebghstl.rdb (weight 1.53986) # T0538.t04.stride-ebghtl.rdb (weight 1.24869) # T0538.t04.str2.rdb (weight 1.54758) # T0538.t04.alpha.rdb (weight 0.659012) # T0538.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0538.t2k.stride-ebghtl.rdb (weight 1.24869) # T0538.t2k.str2.rdb (weight 1.54758) # T0538.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 T0538.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0538 # 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 T0538.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 9.40932 # # ============================================ # Comments from T0538.t04.stride-ebghtl.rdb # ============================================ # TARGET T0538 # 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 T0538.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 9.40932 # # ============================================ # Comments from T0538.t04.str2.rdb # ============================================ # TARGET T0538 # 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 T0538.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 9.40932 # # ============================================ # Comments from T0538.t04.alpha.rdb # ============================================ # TARGET T0538 # 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 T0538.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 9.40932 # # ============================================ # Comments from T0538.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0538 # 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 T0538.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 23 # # ============================================ # Comments from T0538.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0538 # 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 T0538.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 23 # # ============================================ # Comments from T0538.t2k.str2.rdb # ============================================ # TARGET T0538 # 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 T0538.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 23 # # ============================================ # Comments from T0538.t2k.alpha.rdb # ============================================ # TARGET T0538 # 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 T0538.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 23 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0609 0.0240 0.9151 2 N 0.1105 0.0378 0.8517 3 L 0.1157 0.1213 0.7630 4 R 0.1190 0.1369 0.7442 5 W 0.1268 0.1037 0.7695 6 T 0.0513 0.0741 0.8746 7 S 0.0050 0.9330 0.0620 8 E 0.0047 0.9442 0.0511 9 A 0.0048 0.9485 0.0467 10 K 0.0048 0.9506 0.0446 11 T 0.0057 0.9363 0.0581 12 K 0.0081 0.8890 0.1029 13 L 0.0275 0.8439 0.1286 14 K 0.0122 0.8269 0.1608 15 N 0.0198 0.6297 0.3505 16 I 0.0678 0.2565 0.6756 17 P 0.0566 0.2062 0.7372 18 F 0.0984 0.2993 0.6023 19 F 0.1757 0.3141 0.5102 20 A 0.1635 0.2566 0.5800 21 R 0.0574 0.2444 0.6982 22 S 0.0102 0.8105 0.1794 23 Q 0.0062 0.8925 0.1013 24 A 0.0060 0.9109 0.0831 25 K 0.0059 0.9339 0.0602 26 A 0.0058 0.9358 0.0585 27 R 0.0050 0.9467 0.0482 28 I 0.0047 0.9550 0.0403 29 E 0.0047 0.9574 0.0379 30 Q 0.0047 0.9551 0.0402 31 L 0.0047 0.9541 0.0413 32 A 0.0048 0.9486 0.0466 33 R 0.0052 0.9131 0.0818 34 Q 0.0072 0.8176 0.1752 35 A 0.0424 0.3976 0.5599 36 E 0.0370 0.0762 0.8868 37 Q 0.0757 0.0625 0.8618 38 D 0.1701 0.1010 0.7290 39 I 0.3775 0.1242 0.4982 40 V 0.3479 0.1572 0.4949 41 T 0.1524 0.2322 0.6154 42 P 0.0163 0.8971 0.0866 43 E 0.0123 0.9077 0.0800 44 L 0.0087 0.9260 0.0653 45 V 0.0049 0.9564 0.0387 46 E 0.0049 0.9558 0.0393 47 Q 0.0047 0.9563 0.0390 48 A 0.0047 0.9532 0.0421 49 R 0.0048 0.9472 0.0480 50 L 0.0053 0.9286 0.0661 51 E 0.0085 0.8643 0.1272 52 F 0.0441 0.5851 0.3708 53 G 0.0373 0.1703 0.7924 54 Q 0.0443 0.0527 0.9030