# This file is the result of combining several RDB files, specifically # T0335.t04.dssp-ebghstl.rdb (weight 1.53986) # T0335.t04.stride-ebghtl.rdb (weight 1.24869) # T0335.t04.str2.rdb (weight 1.54758) # T0335.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 T0335.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ # Comments from T0335.t04.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 12.359 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0506 0.1928 0.7566 2 I 0.0652 0.3185 0.6163 3 S 0.0351 0.5474 0.4175 4 N 0.0098 0.8491 0.1411 5 A 0.0071 0.9164 0.0765 6 K 0.0049 0.9444 0.0506 7 I 0.0047 0.9514 0.0439 8 A 0.0047 0.9546 0.0407 9 R 0.0047 0.9548 0.0405 10 I 0.0047 0.9573 0.0380 11 N 0.0047 0.9586 0.0367 12 E 0.0047 0.9569 0.0384 13 L 0.0047 0.9486 0.0467 14 A 0.0047 0.9297 0.0655 15 A 0.0048 0.8889 0.1063 16 K 0.0064 0.8521 0.1415 17 A 0.0149 0.8068 0.1783 18 K 0.0152 0.7557 0.2291 19 A 0.0310 0.5889 0.3801 20 G 0.0317 0.1838 0.7845 21 V 0.0556 0.0876 0.8569 22 I 0.1282 0.0196 0.8523 23 T 0.0619 0.0208 0.9173 24 E 0.0048 0.9439 0.0513 25 E 0.0047 0.9533 0.0420 26 E 0.0047 0.9564 0.0389 27 K 0.0047 0.9593 0.0361 28 A 0.0046 0.9589 0.0365 29 E 0.0046 0.9552 0.0402 30 Q 0.0047 0.9568 0.0386 31 Q 0.0046 0.9574 0.0379 32 K 0.0047 0.9527 0.0427 33 L 0.0047 0.9503 0.0451 34 R 0.0047 0.9577 0.0376 35 Q 0.0047 0.9600 0.0354 36 E 0.0049 0.9569 0.0382 37 Y 0.0048 0.9531 0.0421 38 L 0.0047 0.9555 0.0398 39 K 0.0048 0.9531 0.0421 40 G 0.0049 0.9443 0.0508 41 F 0.0050 0.9389 0.0561 42 R 0.0052 0.9498 0.0450 43 S 0.0051 0.9483 0.0467 44 S 0.0052 0.9369 0.0579 45 M 0.0054 0.9358 0.0588 46 K 0.0060 0.9236 0.0704 47 N 0.0098 0.8586 0.1315 48 T 0.0189 0.7334 0.2478 49 L 0.1022 0.5214 0.3763 50 K 0.1282 0.3483 0.5234 51 S 0.2330 0.2037 0.5633 52 V 0.6335 0.0409 0.3256 53 K 0.8236 0.0180 0.1583 54 I 0.8799 0.0077 0.1124 55 I 0.7733 0.0127 0.2141 56 D 0.1709 0.0140 0.8150 57 P 0.0114 0.1254 0.8632 58 E 0.0383 0.0450 0.9166 59 G 0.0547 0.0561 0.8892 60 N 0.0818 0.0822 0.8360 61 D 0.2831 0.0889 0.6280 62 V 0.2412 0.0546 0.7042 63 T 0.0877 0.0361 0.8761 64 P 0.0089 0.9079 0.0833 65 E 0.0048 0.9449 0.0504 66 K 0.0047 0.9497 0.0456 67 L 0.0056 0.9401 0.0543 68 K 0.0048 0.9399 0.0553 69 R 0.0048 0.9432 0.0520 70 E 0.0050 0.9335 0.0615 71 Q 0.0067 0.9094 0.0839 72 R 0.0088 0.8603 0.1309 73 N 0.0101 0.7440 0.2459 74 N 0.0344 0.4822 0.4834 75 K 0.0366 0.3740 0.5894 76 L 0.0795 0.3345 0.5859 77 H 0.1058 0.3389 0.5553 78 L 0.0958 0.3768 0.5275 79 E 0.0831 0.3791 0.5378 80 H 0.0839 0.3458 0.5703 81 H 0.0786 0.3048 0.6166 82 H 0.0697 0.2211 0.7092 83 H 0.0713 0.1492 0.7795 84 H 0.0586 0.1020 0.8394 85 H 0.0502 0.0464 0.9034