# This file is the result of combining several RDB files, specifically # T0185.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0185.t2k.stride-ebghtl.rdb (weight 1.24869) # T0185.t2k.str.rdb (weight 1.53983) # T0185.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 T0185.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0185 # 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 T0185.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 T0185.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0185 # 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 T0185.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 T0185.t2k.str.rdb # ============================================ # TARGET T0185 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0185.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 T0185.t2k.alpha.rdb # ============================================ # TARGET T0185 # 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 T0185.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 S 0.0476 0.0463 0.9061 2 R 0.1400 0.1551 0.7049 3 L 0.1377 0.2151 0.6472 4 E 0.1318 0.2455 0.6227 5 R 0.0883 0.2660 0.6457 6 E 0.0554 0.3040 0.6406 7 D 0.0516 0.2696 0.6789 8 G 0.0423 0.2857 0.6720 9 N 0.0565 0.3840 0.5596 10 F 0.0454 0.6687 0.2859 11 A 0.0338 0.7540 0.2122 12 K 0.0392 0.7552 0.2056 13 A 0.0487 0.7598 0.1915 14 L 0.0878 0.6696 0.2426 15 Q 0.1168 0.5778 0.3054 16 L 0.1274 0.5089 0.3637 17 A 0.1169 0.4769 0.4062 18 D 0.0971 0.4372 0.4657 19 E 0.1995 0.4133 0.3872 20 V 0.4307 0.2968 0.2725 21 V 0.5217 0.2888 0.1895 22 V 0.4716 0.3702 0.1582 23 T 0.3544 0.4590 0.1865 24 E 0.3077 0.4854 0.2069 25 V 0.2408 0.5229 0.2363 26 Y 0.1808 0.5490 0.2702 27 D 0.1102 0.6090 0.2809 28 A 0.0607 0.6946 0.2447 29 F 0.0639 0.6874 0.2487 30 E 0.0589 0.6722 0.2689 31 E 0.0490 0.6424 0.3086 32 K 0.0508 0.5789 0.3703 33 K 0.0511 0.4529 0.4960 34 N 0.0546 0.3013 0.6441 35 G 0.0655 0.1674 0.7672 36 I 0.1367 0.1749 0.6884 37 S 0.1490 0.2227 0.6283 38 G 0.1251 0.3965 0.4783 39 K 0.1679 0.5316 0.3005 40 M 0.2691 0.5219 0.2090 41 I 0.2408 0.5702 0.1890 42 W 0.1381 0.6705 0.1914 43 D 0.0621 0.7303 0.2076 44 S 0.0449 0.7106 0.2445 45 L 0.0426 0.7212 0.2362 46 K 0.0414 0.6932 0.2654 47 S 0.0337 0.6198 0.3465 48 L 0.0474 0.4077 0.5449 49 G 0.0473 0.1539 0.7988 50 K 0.0351 0.0479 0.9170