# This file is the result of combining several RDB files, specifically # T0303.t06.dssp-ebghstl.rdb (weight 1.53986) # T0303.t06.stride-ebghtl.rdb (weight 1.24869) # T0303.t06.str2.rdb (weight 1.54758) # T0303.t06.alpha.rdb (weight 0.659012) # T0303.t04.dssp-ebghstl.rdb (weight 1.53986) # T0303.t04.stride-ebghtl.rdb (weight 1.24869) # T0303.t04.str2.rdb (weight 1.54758) # T0303.t04.alpha.rdb (weight 0.659012) # T0303.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0303.t2k.stride-ebghtl.rdb (weight 1.24869) # T0303.t2k.str2.rdb (weight 1.54758) # T0303.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 T0303.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.str2.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t06.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.7784 # # ============================================ # Comments from T0303.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.str2.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 115 # # ============================================ # Comments from T0303.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 115 # # ============================================ # Comments from T0303.t2k.str2.rdb # ============================================ # TARGET T0303 # 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 T0303.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 115 # # ============================================ # Comments from T0303.t2k.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 115 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.0476 0.1382 0.8143 2 S 0.0538 0.1578 0.7885 3 L 0.0290 0.6260 0.3450 4 P 0.0154 0.7401 0.2445 5 D 0.0189 0.8233 0.1578 6 L 0.0048 0.9520 0.0432 7 A 0.0047 0.9588 0.0365 8 L 0.0047 0.9594 0.0358 9 S 0.0047 0.9602 0.0351 10 I 0.0047 0.9593 0.0360 11 N 0.0047 0.9594 0.0359 12 S 0.0047 0.9598 0.0355 13 A 0.0047 0.9600 0.0354 14 L 0.0048 0.9566 0.0386 15 K 0.0051 0.9409 0.0539 16 D 0.0060 0.8621 0.1318 17 V 0.0439 0.4282 0.5279 18 N 0.0328 0.0412 0.9260 19 L 0.0578 0.0186 0.9236 20 P 0.0757 0.0265 0.8978 21 Q 0.1203 0.0463 0.8334 22 A 0.1398 0.0242 0.8359 23 S 0.1017 0.0336 0.8647 24 E 0.0056 0.9251 0.0693 25 N 0.0048 0.9382 0.0570 26 L 0.0050 0.9396 0.0554 27 V 0.0064 0.9439 0.0497 28 M 0.0069 0.9370 0.0561 29 T 0.0066 0.9231 0.0703 30 W 0.0101 0.8859 0.1039 31 I 0.0225 0.7624 0.2151 32 G 0.0208 0.6353 0.3440 33 N 0.0117 0.5569 0.4314 34 G 0.0087 0.6929 0.2985 35 A 0.0047 0.9136 0.0816 36 D 0.0047 0.9559 0.0394 37 V 0.0047 0.9590 0.0363 38 L 0.0047 0.9596 0.0357 39 S 0.0047 0.9568 0.0385 40 Q 0.0048 0.9509 0.0443 41 R 0.0049 0.9342 0.0609 42 A 0.0057 0.9154 0.0789 43 V 0.0078 0.8507 0.1414 44 D 0.0079 0.7844 0.2077 45 W 0.0175 0.6252 0.3573 46 A 0.0370 0.4702 0.4928 47 C 0.0428 0.2568 0.7004 48 T 0.0517 0.2058 0.7425 49 Q 0.0512 0.2161 0.7327 50 A 0.0494 0.2823 0.6683 51 E 0.0291 0.4555 0.5154 52 K 0.0270 0.6070 0.3659 53 E 0.0136 0.7225 0.2639 54 L 0.0141 0.7795 0.2065 55 T 0.0096 0.8295 0.1608 56 E 0.0078 0.8831 0.1091 57 D 0.0072 0.8970 0.0958 58 E 0.0069 0.8976 0.0955 59 F 0.0061 0.9024 0.0916 60 K 0.0054 0.9331 0.0616 61 Y 0.0049 0.9446 0.0505 62 F 0.0049 0.9485 0.0467 63 K 0.0049 0.9443 0.0508 64 R 0.0049 0.9465 0.0486 65 Q 0.0050 0.9414 0.0537 66 F 0.0056 0.9239 0.0705 67 G 0.0074 0.8918 0.1008 68 F 0.0086 0.8588 0.1326 69 Y 0.0134 0.7800 0.2066 70 Y 0.0274 0.6245 0.3482 71 G 0.0408 0.4465 0.5127 72 E 0.0442 0.3338 0.6221 73 N 0.0570 0.2981 0.6449 74 L 0.1261 0.1551 0.7188 75 C 0.2446 0.0699 0.6855 76 N 0.3249 0.0426 0.6325 77 I 0.2685 0.0497 0.6818 78 S 0.1131 0.0212 0.8657 79 R 0.0503 0.0301 0.9196