# This file is the result of combining several RDB files, specifically # T0349.t04.dssp-ebghstl.rdb (weight 1.53986) # T0349.t04.stride-ebghtl.rdb (weight 1.24869) # T0349.t04.str2.rdb (weight 1.54758) # T0349.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 T0349.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t04.stride-ebghtl.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t04.str2.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t04.alpha.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0522 0.4140 0.5338 2 R 0.1380 0.5268 0.3352 3 E 0.2603 0.5341 0.2056 4 L 0.2027 0.6263 0.1710 5 L 0.1996 0.6125 0.1879 6 R 0.1476 0.4595 0.3929 7 T 0.0836 0.3202 0.5962 8 N 0.0254 0.2472 0.7274 9 D 0.0495 0.4543 0.4963 10 A 0.0225 0.8956 0.0819 11 V 0.0091 0.9460 0.0449 12 L 0.0107 0.9501 0.0391 13 L 0.0083 0.9525 0.0392 14 S 0.0078 0.9501 0.0420 15 A 0.0058 0.9498 0.0443 16 V 0.0058 0.9502 0.0440 17 G 0.0053 0.9494 0.0452 18 A 0.0061 0.9396 0.0543 19 L 0.0074 0.9080 0.0846 20 L 0.0216 0.7588 0.2196 21 D 0.0336 0.4141 0.5523 22 G 0.0287 0.2109 0.7605 23 A 0.0386 0.1993 0.7621 24 D 0.0594 0.1313 0.8093 25 I 0.1998 0.0853 0.7150 26 G 0.2097 0.1058 0.6845 27 H 0.6870 0.0624 0.2506 28 L 0.8186 0.0372 0.1442 29 V 0.8379 0.0366 0.1255 30 L 0.7037 0.0516 0.2446 31 D 0.3495 0.0516 0.5989 32 Q 0.0905 0.2177 0.6918 33 N 0.0852 0.1818 0.7330 34 M 0.1827 0.1880 0.6293 35 S 0.2583 0.1809 0.5607 36 I 0.3611 0.2667 0.3722 37 L 0.3767 0.2625 0.3608 38 E 0.2880 0.2285 0.4836 39 G 0.2039 0.1420 0.6541 40 S 0.2192 0.1519 0.6289 41 L 0.2970 0.1813 0.5217 42 G 0.3471 0.1239 0.5290 43 V 0.4604 0.0888 0.4509 44 I 0.3980 0.0388 0.5632 45 P 0.4090 0.0567 0.5342 46 R 0.4515 0.1134 0.4351 47 R 0.6508 0.1099 0.2393 48 V 0.7737 0.0778 0.1485 49 L 0.7780 0.0591 0.1629 50 V 0.6222 0.0475 0.3303 51 H 0.2197 0.0524 0.7279 52 E 0.0137 0.6541 0.3322 53 D 0.0094 0.6844 0.3062 54 D 0.0130 0.7355 0.2515 55 L 0.0078 0.8803 0.1119 56 A 0.0063 0.9166 0.0771 57 G 0.0051 0.9280 0.0669 58 A 0.0050 0.9474 0.0476 59 R 0.0047 0.9571 0.0382 60 R 0.0047 0.9579 0.0374 61 L 0.0047 0.9583 0.0370 62 L 0.0047 0.9549 0.0404 63 T 0.0050 0.9384 0.0566 64 D 0.0059 0.9054 0.0887 65 A 0.0440 0.6106 0.3453 66 G 0.0419 0.1108 0.8473 67 L 0.0687 0.0856 0.8457 68 A 0.0860 0.1625 0.7516 69 H 0.0833 0.3979 0.5188 70 E 0.0966 0.4665 0.4370 71 L 0.1017 0.4207 0.4777 72 R 0.0890 0.2591 0.6519 73 S 0.0582 0.1743 0.7675 74 D 0.0369 0.1149 0.8482 75 D 0.0396 0.0636 0.8968