# This file is the result of combining several RDB files, specifically # T0221.t04.dssp-ebghstl.rdb (weight 1.53986) # T0221.t04.stride-ebghtl.rdb (weight 1.24869) # T0221.t04.str2.rdb (weight 1.54758) # T0221.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 T0221.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0221 # 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 T0221.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 338.336 # # ============================================ # Comments from T0221.t04.stride-ebghtl.rdb # ============================================ # TARGET T0221 # 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 T0221.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 338.336 # # ============================================ # Comments from T0221.t04.str2.rdb # ============================================ # TARGET T0221 # 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 T0221.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 338.336 # # ============================================ # Comments from T0221.t04.alpha.rdb # ============================================ # TARGET T0221 # 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 T0221.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 338.336 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0630 0.0430 0.8940 2 K 0.0805 0.0567 0.8629 3 T 0.0902 0.0510 0.8588 4 I 0.0781 0.0526 0.8693 5 Q 0.0668 0.0465 0.8867 6 P 0.0660 0.0961 0.8379 7 C 0.0963 0.1003 0.8034 8 S 0.0753 0.1328 0.7919 9 V 0.0077 0.8651 0.1272 10 E 0.0052 0.9425 0.0523 11 D 0.0047 0.9567 0.0386 12 I 0.0047 0.9600 0.0353 13 Q 0.0047 0.9611 0.0342 14 S 0.0046 0.9617 0.0337 15 W 0.0046 0.9615 0.0339 16 L 0.0047 0.9604 0.0350 17 I 0.0047 0.9607 0.0347 18 D 0.0046 0.9617 0.0337 19 Q 0.0047 0.9592 0.0361 20 F 0.0047 0.9581 0.0372 21 A 0.0048 0.9577 0.0375 22 Q 0.0052 0.9500 0.0448 23 Q 0.0074 0.9108 0.0818 24 L 0.0475 0.6224 0.3301 25 D 0.0405 0.0445 0.9150 26 V 0.0744 0.0144 0.9112 27 D 0.0859 0.0086 0.9055 28 P 0.0070 0.7209 0.2721 29 D 0.0094 0.6991 0.2915 30 D 0.0262 0.6743 0.2995 31 I 0.1996 0.1176 0.6827 32 D 0.1318 0.0521 0.8161 33 M 0.0186 0.6248 0.3566 34 E 0.0188 0.6125 0.3687 35 E 0.0367 0.5590 0.4043 36 S 0.0625 0.5003 0.4371 37 F 0.0316 0.6919 0.2765 38 D 0.0199 0.7109 0.2692 39 N 0.0242 0.6643 0.3116 40 Y 0.0697 0.3431 0.5872 41 D 0.0649 0.0920 0.8431 42 L 0.1011 0.1119 0.7870 43 N 0.1099 0.1343 0.7558 44 S 0.0321 0.7230 0.2449 45 S 0.0063 0.9283 0.0654 46 K 0.0051 0.9484 0.0465 47 A 0.0047 0.9598 0.0355 48 L 0.0047 0.9605 0.0349 49 I 0.0046 0.9610 0.0344 50 L 0.0047 0.9592 0.0361 51 L 0.0048 0.9573 0.0380 52 G 0.0048 0.9562 0.0390 53 R 0.0049 0.9561 0.0389 54 L 0.0052 0.9514 0.0434 55 E 0.0063 0.9494 0.0443 56 K 0.0064 0.9393 0.0543 57 W 0.0119 0.8885 0.0995 58 L 0.0497 0.5636 0.3867 59 G 0.0291 0.0787 0.8922 60 K 0.0814 0.0539 0.8647 61 E 0.1933 0.0379 0.7688 62 L 0.1848 0.0274 0.7878 63 N 0.1211 0.0169 0.8620 64 P 0.0895 0.5919 0.3186 65 V 0.1905 0.6136 0.1959 66 L 0.3459 0.5487 0.1054 67 I 0.4237 0.4454 0.1310 68 F 0.3541 0.2967 0.3492 69 N 0.1883 0.1763 0.6355 70 Y 0.0954 0.0381 0.8665 71 P 0.0855 0.0549 0.8596 72 T 0.0812 0.0600 0.8588 73 I 0.0047 0.9563 0.0390 74 A 0.0046 0.9612 0.0342 75 Q 0.0047 0.9609 0.0345 76 L 0.0047 0.9607 0.0346 77 A 0.0047 0.9606 0.0347 78 K 0.0047 0.9577 0.0376 79 R 0.0048 0.9538 0.0414 80 L 0.0049 0.9458 0.0492 81 G 0.0051 0.9324 0.0625 82 E 0.0058 0.8931 0.1011 83 L 0.0080 0.7932 0.1987 84 Y 0.0185 0.5298 0.4516 85 L 0.0200 0.1305 0.8495