# This file is the result of combining several RDB files, specifically # T0348.t06.dssp-ebghstl.rdb (weight 1.53986) # T0348.t06.stride-ebghtl.rdb (weight 1.24869) # T0348.t06.str2.rdb (weight 1.54758) # T0348.t06.alpha.rdb (weight 0.659012) # T0348.t04.dssp-ebghstl.rdb (weight 1.53986) # T0348.t04.stride-ebghtl.rdb (weight 1.24869) # T0348.t04.str2.rdb (weight 1.54758) # T0348.t04.alpha.rdb (weight 0.659012) # T0348.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0348.t2k.stride-ebghtl.rdb (weight 1.24869) # T0348.t2k.str2.rdb (weight 1.54758) # T0348.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 T0348.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 29.7212 # # ============================================ # Comments from T0348.t06.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 29.7212 # # ============================================ # Comments from T0348.t06.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 29.7212 # # ============================================ # Comments from T0348.t06.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 29.7212 # # ============================================ # Comments from T0348.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 28.2264 # # ============================================ # Comments from T0348.t04.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 28.2264 # # ============================================ # Comments from T0348.t04.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 28.2264 # # ============================================ # Comments from T0348.t04.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 28.2264 # # ============================================ # Comments from T0348.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 159 # # ============================================ # Comments from T0348.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0348 # 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 T0348.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 159 # # ============================================ # Comments from T0348.t2k.str2.rdb # ============================================ # TARGET T0348 # 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 T0348.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 159 # # ============================================ # Comments from T0348.t2k.alpha.rdb # ============================================ # TARGET T0348 # 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 T0348.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 159 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0480 0.0515 0.9006 2 D 0.0720 0.0953 0.8327 3 A 0.0089 0.7625 0.2285 4 K 0.0109 0.8296 0.1595 5 F 0.0091 0.9085 0.0825 6 L 0.0072 0.9414 0.0513 7 E 0.0079 0.9312 0.0609 8 I 0.0085 0.9195 0.0719 9 L 0.0131 0.8415 0.1453 10 V 0.0298 0.6631 0.3070 11 C 0.0548 0.1933 0.7519 12 P 0.0353 0.2602 0.7045 13 L 0.0487 0.3283 0.6229 14 C 0.0968 0.2323 0.6710 15 K 0.0940 0.1122 0.7938 16 G 0.1361 0.0463 0.8175 17 P 0.3052 0.0404 0.6543 18 L 0.5920 0.0271 0.3809 19 V 0.7413 0.0152 0.2434 20 F 0.6998 0.0198 0.2804 21 D 0.4350 0.0340 0.5310 22 K 0.0695 0.2750 0.6555 23 S 0.0437 0.2362 0.7201 24 K 0.0848 0.2096 0.7055 25 D 0.1207 0.1180 0.7614 26 E 0.6217 0.0514 0.3269 27 L 0.7957 0.0302 0.1741 28 I 0.7324 0.0356 0.2320 29 C 0.4518 0.0396 0.5086 30 K 0.0571 0.2874 0.6555 31 G 0.0263 0.3312 0.6425 32 D 0.0468 0.3152 0.6380 33 R 0.0904 0.1775 0.7321 34 L 0.2925 0.1240 0.5835 35 A 0.4505 0.0761 0.4734 36 F 0.4603 0.0230 0.5168 37 P 0.4184 0.0281 0.5534 38 I 0.3026 0.0924 0.6050 39 K 0.1800 0.1242 0.6959 40 D 0.0803 0.0705 0.8491 41 G 0.0519 0.0526 0.8955 42 I 0.2074 0.0448 0.7478 43 P 0.3317 0.0655 0.6028 44 M 0.3946 0.0990 0.5064 45 M 0.4535 0.0646 0.4819 46 L 0.2104 0.0625 0.7271 47 E 0.0206 0.7309 0.2485 48 S 0.0073 0.8684 0.1243 49 E 0.0084 0.8665 0.1251 50 A 0.0245 0.8076 0.1679 51 R 0.0374 0.7992 0.1634 52 E 0.0719 0.5715 0.3566 53 L 0.0835 0.2925 0.6240 54 A 0.0727 0.0660 0.8612 55 P 0.0231 0.3958 0.5811 56 E 0.0279 0.4149 0.5572 57 E 0.0797 0.3622 0.5582 58 E 0.1811 0.2405 0.5784 59 V 0.1515 0.1779 0.6706 60 K 0.1366 0.1306 0.7327 61 L 0.0869 0.1768 0.7364 62 E 0.0797 0.2252 0.6950 63 H 0.1355 0.2535 0.6110 64 H 0.1693 0.2327 0.5980 65 H 0.1582 0.2040 0.6378 66 H 0.1265 0.1419 0.7316 67 H 0.0984 0.0752 0.8264 68 H 0.0499 0.0360 0.9140