# This file is the result of combining several RDB files, specifically # T0379.t04.dssp-ebghstl.rdb (weight 1.53986) # T0379.t04.stride-ebghtl.rdb (weight 1.24869) # T0379.t04.str2.rdb (weight 1.54758) # T0379.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 T0379.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ # Comments from T0379.t04.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0916 0.1353 0.7731 2 L 0.1107 0.1447 0.7446 3 N 0.0832 0.1240 0.7927 4 R 0.0350 0.5197 0.4453 5 E 0.0202 0.7942 0.1857 6 E 0.0255 0.7991 0.1754 7 S 0.0424 0.7890 0.1687 8 I 0.0627 0.8061 0.1313 9 R 0.0671 0.7951 0.1378 10 R 0.0880 0.7476 0.1644 11 F 0.1355 0.6607 0.2038 12 K 0.1475 0.5980 0.2545 13 A 0.2264 0.5339 0.2397 14 I 0.2103 0.3327 0.4569 15 G 0.1770 0.1244 0.6986 16 V 0.2405 0.2072 0.5523 17 A 0.3040 0.2309 0.4651 18 D 0.2624 0.2499 0.4877 19 I 0.0130 0.8905 0.0966 20 E 0.0085 0.9157 0.0758 21 E 0.0079 0.8912 0.1009 22 M 0.0177 0.7945 0.1878 23 L 0.0376 0.6232 0.3393 24 D 0.0448 0.4077 0.5475 25 P 0.0057 0.7647 0.2296 26 Y 0.0120 0.7367 0.2512 27 L 0.0296 0.7527 0.2176 28 Q 0.0409 0.6677 0.2915 29 K 0.0485 0.4096 0.5419 30 G 0.0784 0.1839 0.7378 31 L 0.2513 0.1168 0.6319 32 F 0.5243 0.1012 0.3745 33 L 0.5753 0.0773 0.3475 34 D 0.4848 0.0582 0.4571 35 L 0.1835 0.3311 0.4854 36 E 0.1062 0.3111 0.5827 37 S 0.0763 0.2057 0.7180 38 G 0.0606 0.1006 0.8388 39 R 0.1295 0.0821 0.7885 40 K 0.1669 0.0916 0.7415 41 S 0.1008 0.1223 0.7769 42 E 0.0218 0.8065 0.1718 43 E 0.0130 0.8997 0.0873 44 E 0.0148 0.9055 0.0798 45 F 0.0213 0.8847 0.0939 46 R 0.0223 0.8884 0.0893 47 T 0.0176 0.8968 0.0856 48 E 0.0176 0.8918 0.0906 49 L 0.0227 0.8795 0.0977 50 S 0.0322 0.8387 0.1292 51 R 0.0353 0.8132 0.1515 52 Y 0.0557 0.7435 0.2008 53 I 0.0765 0.5671 0.3565 54 G 0.0679 0.2986 0.6336 55 K 0.1089 0.3532 0.5379 56 E 0.2134 0.3873 0.3994 57 L 0.2303 0.3436 0.4261 58 T 0.1947 0.3696 0.4358 59 Y 0.0570 0.8230 0.1200 60 Q 0.0279 0.9032 0.0690 61 Q 0.0320 0.9057 0.0623 62 V 0.0171 0.9260 0.0570 63 Y 0.0105 0.9405 0.0491 64 D 0.0091 0.9391 0.0518 65 A 0.0109 0.9278 0.0613 66 L 0.0112 0.9169 0.0719 67 L 0.0191 0.8676 0.1133 68 G 0.0252 0.7442 0.2306 69 F 0.0435 0.6537 0.3028 70 L 0.0944 0.4597 0.4459 71 E 0.0905 0.3201 0.5894 72 E 0.0640 0.1890 0.7470