# This file is the result of combining several RDB files, specifically # T0354.t06.dssp-ebghstl.rdb (weight 1.53986) # T0354.t06.stride-ebghtl.rdb (weight 1.24869) # T0354.t06.str2.rdb (weight 1.54758) # T0354.t06.alpha.rdb (weight 0.659012) # T0354.t04.dssp-ebghstl.rdb (weight 1.53986) # T0354.t04.stride-ebghtl.rdb (weight 1.24869) # T0354.t04.str2.rdb (weight 1.54758) # T0354.t04.alpha.rdb (weight 0.659012) # T0354.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0354.t2k.stride-ebghtl.rdb (weight 1.24869) # T0354.t2k.str2.rdb (weight 1.54758) # T0354.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 T0354.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.stride-ebghtl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.str2.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.alpha.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.stride-ebghtl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.str2.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t04.alpha.rdb # ============================================ # TARGET T0354 # 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 T0354.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 83.2997 # # ============================================ # Comments from T0354.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 305 # # ============================================ # Comments from T0354.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 305 # # ============================================ # Comments from T0354.t2k.str2.rdb # ============================================ # TARGET T0354 # 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 T0354.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 305 # # ============================================ # Comments from T0354.t2k.alpha.rdb # ============================================ # TARGET T0354 # 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 T0354.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 305 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0427 0.1272 0.8301 2 E 0.0736 0.2581 0.6683 3 I 0.0135 0.7832 0.2034 4 Q 0.0052 0.9268 0.0680 5 E 0.0055 0.9404 0.0541 6 I 0.0047 0.9484 0.0469 7 S 0.0047 0.9559 0.0395 8 K 0.0047 0.9568 0.0384 9 L 0.0047 0.9575 0.0378 10 A 0.0047 0.9581 0.0373 11 I 0.0047 0.9569 0.0384 12 E 0.0047 0.9496 0.0456 13 A 0.0048 0.9333 0.0619 14 L 0.0054 0.9148 0.0798 15 E 0.0058 0.8313 0.1630 16 D 0.0100 0.6148 0.3752 17 I 0.0430 0.3529 0.6041 18 K 0.0760 0.1706 0.7533 19 G 0.0859 0.1281 0.7860 20 K 0.0705 0.1642 0.7653 21 D 0.2248 0.0764 0.6988 22 I 0.6016 0.0147 0.3837 23 I 0.8492 0.0079 0.1429 24 E 0.9110 0.0042 0.0848 25 L 0.8738 0.0067 0.1195 26 D 0.7076 0.0072 0.2852 27 T 0.2124 0.1562 0.6314 28 S 0.0757 0.1946 0.7297 29 K 0.0619 0.2328 0.7054 30 L 0.1484 0.1496 0.7020 31 T 0.2464 0.0902 0.6634 32 S 0.2859 0.1334 0.5807 33 L 0.2726 0.2579 0.4695 34 F 0.4137 0.1291 0.4572 35 Q 0.5693 0.0878 0.3429 36 R 0.8693 0.0162 0.1145 37 M 0.9077 0.0116 0.0807 38 I 0.9229 0.0090 0.0680 39 V 0.9013 0.0180 0.0807 40 A 0.8251 0.0231 0.1518 41 T 0.4244 0.0419 0.5337 42 G 0.1153 0.0511 0.8336 43 D 0.0486 0.0804 0.8709 44 S 0.0653 0.1757 0.7589 45 N 0.0079 0.8365 0.1556 46 R 0.0074 0.9273 0.0652 47 Q 0.0058 0.9502 0.0441 48 V 0.0047 0.9594 0.0359 49 K 0.0047 0.9602 0.0351 50 A 0.0047 0.9590 0.0363 51 L 0.0047 0.9580 0.0373 52 A 0.0047 0.9589 0.0364 53 N 0.0049 0.9553 0.0398 54 S 0.0048 0.9527 0.0425 55 V 0.0047 0.9561 0.0391 56 Q 0.0047 0.9577 0.0375 57 V 0.0047 0.9583 0.0369 58 K 0.0048 0.9559 0.0393 59 L 0.0056 0.9515 0.0430 60 K 0.0051 0.9408 0.0542 61 E 0.0066 0.8969 0.0965 62 A 0.0428 0.3810 0.5762 63 G 0.0351 0.0296 0.9353 64 V 0.0732 0.0180 0.9088 65 D 0.2061 0.0228 0.7711 66 I 0.2892 0.0478 0.6629 67 V 0.3837 0.0650 0.5512 68 G 0.4539 0.0450 0.5011 69 S 0.4630 0.0582 0.4788 70 E 0.3560 0.0816 0.5624 71 G 0.2515 0.0827 0.6657 72 H 0.1976 0.0778 0.7246 73 E 0.1773 0.0745 0.7482 74 S 0.0999 0.0705 0.8296 75 G 0.1165 0.0413 0.8422 76 E 0.4643 0.0153 0.5204 77 W 0.8639 0.0035 0.1326 78 V 0.9135 0.0042 0.0823 79 L 0.9271 0.0031 0.0698 80 V 0.8888 0.0061 0.1052 81 D 0.7478 0.0053 0.2469 82 A 0.2787 0.0841 0.6372 83 G 0.1113 0.0791 0.8096 84 D 0.1891 0.0911 0.7198 85 V 0.6455 0.0270 0.3275 86 V 0.8613 0.0138 0.1249 87 V 0.8859 0.0163 0.0978 88 H 0.8598 0.0265 0.1137 89 V 0.7408 0.0322 0.2270 90 M 0.4257 0.0254 0.5489 91 L 0.1382 0.0203 0.8415 92 P 0.0209 0.7875 0.1917 93 A 0.0070 0.8772 0.1158 94 V 0.0086 0.8744 0.1170 95 R 0.0128 0.8578 0.1294 96 D 0.0169 0.8056 0.1775 97 Y 0.0291 0.7870 0.1839 98 Y 0.0592 0.6913 0.2495 99 D 0.0995 0.5906 0.3099 100 I 0.0094 0.8935 0.0971 101 E 0.0095 0.8995 0.0911 102 A 0.0128 0.8879 0.0993 103 L 0.0166 0.8381 0.1453 104 W 0.0307 0.7043 0.2650 105 G 0.0320 0.4727 0.4953 106 G 0.0424 0.2607 0.6970 107 Q 0.0662 0.0684 0.8654 108 K 0.0937 0.0672 0.8391 109 P 0.2267 0.1051 0.6682 110 S 0.3024 0.0921 0.6055 111 F 0.3172 0.0962 0.5866 112 A 0.1840 0.2165 0.5995 113 V 0.0977 0.2749 0.6274 114 G 0.0648 0.2961 0.6390 115 A 0.0512 0.2302 0.7186 116 A 0.0564 0.1949 0.7487 117 K 0.0623 0.1412 0.7966 118 P 0.0633 0.1956 0.7411 119 W 0.0637 0.2596 0.6768 120 S 0.0162 0.7385 0.2454 121 A 0.0165 0.8149 0.1686 122 V 0.0319 0.8289 0.1392 123 L 0.0398 0.8292 0.1310 124 E 0.0385 0.8044 0.1572 125 H 0.0516 0.7462 0.2022 126 H 0.0758 0.6102 0.3140 127 H 0.0795 0.4736 0.4469 128 H 0.0781 0.2761 0.6458 129 H 0.0803 0.1371 0.7826 130 H 0.0429 0.0473 0.9098