# This file is the result of combining several RDB files, specifically # T0381.t04.dssp-ebghstl.rdb (weight 1.53986) # T0381.t04.stride-ebghtl.rdb (weight 1.24869) # T0381.t04.str2.rdb (weight 1.54758) # T0381.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 T0381.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ # Comments from T0381.t04.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 175.891 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0777 0.0225 0.8998 2 T 0.0826 0.0271 0.8903 3 A 0.0566 0.0915 0.8519 4 T 0.0621 0.0793 0.8586 5 E 0.0727 0.0495 0.8778 6 P 0.0684 0.0683 0.8633 7 T 0.0717 0.2233 0.7050 8 E 0.0386 0.4891 0.4723 9 K 0.0421 0.4640 0.4939 10 I 0.0692 0.2467 0.6842 11 L 0.0766 0.0489 0.8744 12 P 0.0596 0.0536 0.8868 13 S 0.0687 0.0302 0.9011 14 P 0.0139 0.4910 0.4950 15 D 0.0178 0.6064 0.3758 16 Y 0.0134 0.8374 0.1493 17 V 0.0080 0.9208 0.0712 18 Q 0.0064 0.9384 0.0551 19 S 0.0060 0.9484 0.0455 20 L 0.0047 0.9585 0.0369 21 A 0.0047 0.9603 0.0351 22 R 0.0047 0.9584 0.0370 23 G 0.0047 0.9599 0.0354 24 L 0.0047 0.9599 0.0354 25 A 0.0047 0.9601 0.0353 26 V 0.0046 0.9587 0.0367 27 I 0.0047 0.9540 0.0413 28 R 0.0048 0.9309 0.0643 29 C 0.0055 0.8935 0.1010 30 F 0.0165 0.7479 0.2356 31 D 0.0404 0.4809 0.4788 32 H 0.0284 0.4565 0.5152 33 R 0.0390 0.3303 0.6307 34 N 0.0437 0.2218 0.7345 35 Q 0.0386 0.2134 0.7480 36 R 0.0901 0.1616 0.7483 37 R 0.1689 0.0646 0.7665 38 T 0.1222 0.0592 0.8186 39 L 0.0048 0.9522 0.0430 40 S 0.0047 0.9611 0.0343 41 D 0.0046 0.9614 0.0340 42 V 0.0046 0.9615 0.0339 43 A 0.0047 0.9587 0.0365 44 R 0.0049 0.9463 0.0488 45 A 0.0057 0.8962 0.0982 46 T 0.0481 0.4813 0.4706 47 D 0.0401 0.0595 0.9005 48 L 0.0521 0.0337 0.9142 49 T 0.0427 0.0827 0.8746 50 R 0.0194 0.6546 0.3260 51 A 0.0118 0.8824 0.1059 52 T 0.0072 0.9168 0.0759 53 A 0.0047 0.9576 0.0377 54 R 0.0047 0.9609 0.0344 55 R 0.0046 0.9609 0.0344 56 F 0.0047 0.9595 0.0359 57 L 0.0047 0.9603 0.0351 58 L 0.0047 0.9602 0.0351 59 T 0.0046 0.9603 0.0350 60 L 0.0047 0.9588 0.0365 61 V 0.0049 0.9474 0.0477 62 E 0.0056 0.9077 0.0867 63 L 0.0392 0.5366 0.4242 64 G 0.0319 0.0832 0.8849 65 Y 0.2159 0.0528 0.7313 66 V 0.7185 0.0282 0.2533 67 A 0.7185 0.0180 0.2636 68 T 0.6566 0.0296 0.3138 69 D 0.2422 0.0302 0.7276 70 G 0.0369 0.0564 0.9067 71 S 0.0941 0.0542 0.8517 72 A 0.4015 0.0451 0.5534 73 F 0.6501 0.0240 0.3259 74 W 0.6980 0.0237 0.2783 75 L 0.4621 0.0415 0.4965 76 T 0.1114 0.0953 0.7932 77 P 0.0069 0.9181 0.0750 78 R 0.0064 0.9395 0.0541 79 V 0.0055 0.9520 0.0425 80 L 0.0057 0.9511 0.0433 81 E 0.0054 0.9461 0.0485 82 L 0.0055 0.9149 0.0796 83 G 0.0059 0.9149 0.0792 84 Y 0.0059 0.9311 0.0630 85 S 0.0059 0.9323 0.0618 86 Y 0.0063 0.9134 0.0803 87 L 0.0104 0.8785 0.1111 88 S 0.0109 0.7632 0.2259 89 S 0.0177 0.5404 0.4419 90 L 0.0525 0.1502 0.7973 91 S 0.0399 0.0740 0.8861