# 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) # 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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0492 0.0313 0.9195 2 D 0.0707 0.0278 0.9015 3 A 0.0060 0.8346 0.1594 4 K 0.0082 0.8236 0.1682 5 F 0.0099 0.8699 0.1202 6 L 0.0205 0.8353 0.1443 7 E 0.0346 0.8422 0.1232 8 I 0.0497 0.8322 0.1182 9 L 0.1006 0.7173 0.1821 10 V 0.1665 0.4677 0.3658 11 C 0.1391 0.1061 0.7548 12 P 0.0829 0.1689 0.7482 13 L 0.1170 0.1483 0.7347 14 C 0.1521 0.0860 0.7618 15 K 0.0975 0.0779 0.8245 16 G 0.1336 0.0382 0.8282 17 P 0.3117 0.0617 0.6266 18 L 0.5513 0.0438 0.4049 19 V 0.8085 0.0243 0.1672 20 F 0.8048 0.0257 0.1695 21 D 0.6122 0.0310 0.3569 22 K 0.2810 0.2317 0.4873 23 S 0.2590 0.1932 0.5479 24 K 0.1171 0.1615 0.7214 25 D 0.1029 0.1037 0.7934 26 E 0.5584 0.0697 0.3719 27 L 0.7532 0.0450 0.2018 28 I 0.7247 0.0385 0.2368 29 C 0.4158 0.0327 0.5514 30 K 0.0608 0.2150 0.7242 31 G 0.0442 0.1817 0.7741 32 D 0.1022 0.2380 0.6598 33 R 0.1554 0.2087 0.6359 34 L 0.3699 0.1279 0.5021 35 A 0.5215 0.0867 0.3918 36 F 0.5276 0.0338 0.4385 37 P 0.4881 0.0366 0.4753 38 I 0.3096 0.1482 0.5422 39 K 0.2312 0.1814 0.5874 40 D 0.0786 0.1366 0.7849 41 G 0.0784 0.0798 0.8418 42 I 0.2639 0.0548 0.6813 43 P 0.5094 0.0763 0.4143 44 M 0.5033 0.1251 0.3716 45 M 0.4360 0.1202 0.4439 46 L 0.2631 0.1174 0.6196 47 E 0.0765 0.5653 0.3583 48 S 0.0396 0.7091 0.2514 49 E 0.0318 0.7343 0.2339 50 A 0.0607 0.6537 0.2856 51 R 0.0896 0.5474 0.3630 52 E 0.1165 0.3744 0.5091 53 L 0.0953 0.1427 0.7619 54 A 0.0576 0.0260 0.9164 55 P 0.0138 0.5656 0.4206 56 E 0.0169 0.6211 0.3620 57 E 0.0369 0.6889 0.2742 58 E 0.0914 0.6560 0.2526 59 V 0.1637 0.5684 0.2678 60 K 0.1744 0.5114 0.3142 61 L 0.1381 0.4967 0.3652 62 E 0.1124 0.4312 0.4564 63 H 0.0843 0.4249 0.4907 64 H 0.0797 0.3381 0.5822 65 H 0.0900 0.2283 0.6817 66 H 0.0860 0.1465 0.7675 67 H 0.0599 0.0779 0.8623 68 H 0.0468 0.0314 0.9218