# This file is the result of combining several RDB files, specifically # T0281.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0281.t2k.stride-ebghtl.rdb (weight 1.24869) # T0281.t2k.str2.rdb (weight 1.54758) # T0281.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 T0281.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0281 # 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 T0281.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 53 # # ============================================ # Comments from T0281.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0281 # 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 T0281.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 53 # # ============================================ # Comments from T0281.t2k.str2.rdb # ============================================ # TARGET T0281 # 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 T0281.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 53 # # ============================================ # Comments from T0281.t2k.alpha.rdb # ============================================ # TARGET T0281 # 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 T0281.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 53 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0641 0.0492 0.8868 2 W 0.1075 0.0555 0.8369 3 M 0.0791 0.0860 0.8349 4 P 0.0897 0.0679 0.8424 5 P 0.1287 0.0371 0.8342 6 R 0.0844 0.0297 0.8859 7 P 0.0090 0.9110 0.0800 8 E 0.0048 0.9495 0.0456 9 E 0.0047 0.9576 0.0377 10 V 0.0047 0.9599 0.0355 11 A 0.0047 0.9606 0.0347 12 R 0.0047 0.9608 0.0345 13 K 0.0047 0.9606 0.0347 14 L 0.0047 0.9577 0.0376 15 R 0.0049 0.9415 0.0535 16 R 0.0068 0.8659 0.1273 17 L 0.0407 0.3374 0.6219 18 G 0.0437 0.0302 0.9262 19 F 0.1693 0.0186 0.8122 20 V 0.6905 0.0215 0.2879 21 E 0.7827 0.0227 0.1946 22 R 0.7449 0.0358 0.2192 23 M 0.6578 0.0265 0.3157 24 A 0.5056 0.0392 0.4551 25 K 0.3307 0.0392 0.6301 26 G 0.2217 0.0323 0.7460 27 G 0.3232 0.0340 0.6428 28 H 0.6904 0.0210 0.2886 29 R 0.8057 0.0140 0.1804 30 L 0.8925 0.0063 0.1012 31 Y 0.8627 0.0104 0.1269 32 T 0.8153 0.0105 0.1742 33 H 0.4517 0.0146 0.5337 34 P 0.0458 0.0857 0.8684 35 D 0.0469 0.0430 0.9101 36 G 0.0793 0.0521 0.8686 37 R 0.3668 0.0141 0.6191 38 I 0.8125 0.0049 0.1826 39 V 0.8083 0.0052 0.1866 40 V 0.7453 0.0064 0.2482 41 V 0.4474 0.0107 0.5420 42 P 0.2100 0.0235 0.7666 43 F 0.0927 0.0275 0.8798 44 H 0.0465 0.1270 0.8265 45 S 0.0334 0.2500 0.7167 46 G 0.0300 0.2837 0.6862 47 E 0.0656 0.1864 0.7480 48 L 0.1236 0.0769 0.7995 49 P 0.0567 0.0701 0.8731 50 K 0.0162 0.7687 0.2150 51 G 0.0090 0.8362 0.1548 52 T 0.0073 0.9117 0.0810 53 F 0.0047 0.9514 0.0439 54 K 0.0049 0.9559 0.0392 55 R 0.0048 0.9563 0.0389 56 I 0.0047 0.9567 0.0386 57 L 0.0049 0.9548 0.0402 58 R 0.0056 0.9367 0.0577 59 D 0.0079 0.8484 0.1437 60 A 0.0466 0.4087 0.5447 61 G 0.0371 0.0459 0.9170 62 L 0.0619 0.0115 0.9266 63 T 0.0601 0.0126 0.9273 64 E 0.0104 0.8512 0.1384 65 E 0.0094 0.8821 0.1085 66 E 0.0115 0.8907 0.0978 67 F 0.0277 0.8128 0.1595 68 H 0.0428 0.6182 0.3390 69 N 0.0343 0.4289 0.5368 70 L 0.0364 0.0965 0.8671