# This file is the result of combining several RDB files, specifically # T0201.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0201.t2k.stride-ebghtl.rdb (weight 1.24869) # T0201.t2k.str2.rdb (weight 1.54758) # T0201.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 T0201.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0201 # 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 T0201.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 1 # # ============================================ # Comments from T0201.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0201 # 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 T0201.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 1 # # ============================================ # Comments from T0201.t2k.str2.rdb # ============================================ # TARGET T0201 # 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 T0201.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 1 # # ============================================ # Comments from T0201.t2k.alpha.rdb # ============================================ # TARGET T0201 # 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 T0201.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1162 0.0254 0.8584 2 I 0.4043 0.0299 0.5659 3 K 0.6605 0.0252 0.3143 4 V 0.7483 0.0230 0.2286 5 T 0.7805 0.0176 0.2019 6 V 0.7491 0.0239 0.2270 7 T 0.5222 0.0582 0.4196 8 N 0.3088 0.1102 0.5810 9 S 0.2915 0.1651 0.5434 10 F 0.4823 0.1438 0.3739 11 F 0.5777 0.1182 0.3040 12 E 0.6142 0.1047 0.2811 13 V 0.5448 0.1064 0.3488 14 T 0.3454 0.1051 0.5495 15 G 0.1979 0.0912 0.7109 16 H 0.1665 0.0784 0.7552 17 A 0.1460 0.0652 0.7889 18 P 0.0873 0.1148 0.7979 19 D 0.0894 0.1575 0.7531 20 K 0.1207 0.2696 0.6097 21 T 0.2441 0.2953 0.4606 22 L 0.3214 0.3475 0.3312 23 C 0.3186 0.3931 0.2883 24 A 0.2452 0.4908 0.2640 25 S 0.2359 0.5226 0.2415 26 V 0.1453 0.6959 0.1588 27 S 0.1153 0.7432 0.1415 28 L 0.0833 0.7789 0.1378 29 L 0.0659 0.7960 0.1381 30 T 0.0414 0.8287 0.1299 31 Q 0.0219 0.8566 0.1216 32 H 0.0232 0.8465 0.1303 33 V 0.0193 0.8720 0.1087 34 A 0.0141 0.8735 0.1124 35 N 0.0159 0.8249 0.1592 36 F 0.0167 0.8166 0.1667 37 L 0.0327 0.7484 0.2189 38 K 0.0315 0.6930 0.2755 39 A 0.0283 0.7177 0.2540 40 E 0.0404 0.6896 0.2699 41 K 0.0460 0.6603 0.2937 42 K 0.0574 0.6326 0.3100 43 A 0.0805 0.5972 0.3223 44 K 0.1198 0.5576 0.3226 45 I 0.1514 0.5101 0.3386 46 K 0.1803 0.4195 0.4001 47 K 0.1388 0.4096 0.4516 48 E 0.1185 0.3400 0.5414 49 S 0.1087 0.2148 0.6766 50 G 0.1422 0.1310 0.7268 51 Y 0.4096 0.0999 0.4905 52 L 0.6619 0.0751 0.2630 53 K 0.7273 0.0660 0.2067 54 V 0.7016 0.0700 0.2284 55 K 0.6413 0.0807 0.2780 56 F 0.4177 0.3073 0.2750 57 E 0.2810 0.4138 0.3052 58 E 0.2267 0.4180 0.3553 59 L 0.1373 0.4945 0.3682 60 E 0.0737 0.5284 0.3979 61 N 0.0582 0.4608 0.4810 62 C 0.1238 0.3872 0.4891 63 E 0.1742 0.4607 0.3652 64 V 0.2026 0.6262 0.1712 65 K 0.1599 0.7195 0.1206 66 V 0.1327 0.7665 0.1008 67 L 0.0695 0.8457 0.0848 68 A 0.0401 0.8812 0.0787 69 A 0.0304 0.8860 0.0836 70 M 0.0259 0.8728 0.1012 71 V 0.0252 0.8684 0.1063 72 R 0.0213 0.8219 0.1568 73 S 0.0246 0.7704 0.2051 74 L 0.0168 0.8213 0.1619 75 K 0.0124 0.8437 0.1440 76 E 0.0114 0.8476 0.1411 77 L 0.0140 0.8318 0.1543 78 E 0.0184 0.7888 0.1929 79 Q 0.0222 0.6873 0.2904 80 K 0.0357 0.5312 0.4331 81 F 0.0765 0.2009 0.7226 82 P 0.0515 0.2650 0.6835 83 S 0.0735 0.3111 0.6154 84 Q 0.2150 0.2357 0.5494 85 I 0.5113 0.0819 0.4068 86 R 0.6797 0.0454 0.2749 87 V 0.7368 0.0451 0.2181 88 E 0.7340 0.0436 0.2223 89 V 0.7253 0.0479 0.2267 90 I 0.5430 0.0714 0.3856 91 D 0.3211 0.0865 0.5924 92 N 0.1247 0.0722 0.8030 93 G 0.0699 0.0517 0.8784 94 S 0.0441 0.0374 0.9185