# This file is the result of combining several RDB files, specifically # T0295.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0295.t2k.stride-ebghtl.rdb (weight 1.24869) # T0295.t2k.str2.rdb (weight 1.54758) # T0295.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 T0295.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 50 # # ============================================ # Comments from T0295.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 50 # # ============================================ # Comments from T0295.t2k.str2.rdb # ============================================ # TARGET T0295 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0295.t2k-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 11.442 # # ============================================ # Comments from T0295.t2k.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 50 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0853 0.0206 0.8941 2 S 0.1049 0.0256 0.8695 3 F 0.1276 0.0320 0.8404 4 L 0.2178 0.0400 0.7422 5 T 0.2646 0.0271 0.7084 6 N 0.1413 0.0204 0.8383 7 F 0.0230 0.7031 0.2739 8 D 0.0163 0.7550 0.2286 9 E 0.0167 0.7962 0.1871 10 W 0.0152 0.8295 0.1553 11 D 0.0106 0.8205 0.1689 12 N 0.0172 0.8310 0.1518 13 L 0.0185 0.8977 0.0838 14 L 0.0349 0.9061 0.0590 15 R 0.0467 0.8947 0.0586 16 I 0.0576 0.8798 0.0626 17 C 0.0757 0.8344 0.0899 18 F 0.0714 0.7652 0.1635 19 S 0.0663 0.6670 0.2666 20 R 0.0804 0.4839 0.4356 21 K 0.0862 0.5379 0.3759 22 R 0.0865 0.4397 0.4737 23 K 0.0929 0.4232 0.4839 24 T 0.2219 0.4141 0.3640 25 L 0.1246 0.6089 0.2665 26 H 0.1698 0.5757 0.2545 27 A 0.1943 0.5832 0.2225 28 I 0.1430 0.5935 0.2636 29 F 0.1320 0.5112 0.3568 30 K 0.0927 0.4502 0.4571 31 R 0.0678 0.5990 0.3332 32 N 0.0171 0.8264 0.1566 33 A 0.0231 0.8705 0.1064 34 V 0.0079 0.9427 0.0495 35 L 0.0053 0.9564 0.0383 36 N 0.0053 0.9585 0.0362 37 M 0.0047 0.9579 0.0374 38 L 0.0051 0.9540 0.0410 39 E 0.0049 0.9478 0.0473 40 H 0.0059 0.8859 0.1082 41 N 0.0082 0.7315 0.2604 42 Y 0.0295 0.6023 0.3682 43 K 0.0869 0.6048 0.3083 44 N 0.1626 0.5980 0.2393 45 W 0.2413 0.5555 0.2032 46 C 0.2741 0.5024 0.2235 47 T 0.2577 0.4286 0.3138 48 L 0.1677 0.3720 0.4602 49 N 0.1390 0.1866 0.6744 50 K 0.1063 0.1105 0.7832 51 Q 0.1895 0.0754 0.7351 52 V 0.1764 0.0498 0.7738 53 P 0.0970 0.0586 0.8443 54 V 0.0538 0.1053 0.8410 55 N 0.0499 0.1191 0.8310 56 F 0.0475 0.1995 0.7530 57 P 0.0610 0.3525 0.5865 58 F 0.0217 0.7644 0.2139 59 K 0.0084 0.8866 0.1050 60 K 0.0064 0.9461 0.0475 61 Y 0.0052 0.9451 0.0497 62 C 0.0051 0.9520 0.0429 63 L 0.0047 0.9589 0.0364 64 D 0.0047 0.9566 0.0386 65 V 0.0047 0.9558 0.0395 66 L 0.0052 0.9441 0.0507 67 E 0.0054 0.9053 0.0893 68 H 0.0107 0.7692 0.2201 69 L 0.0468 0.4591 0.4941 70 D 0.0483 0.3335 0.6182 71 M 0.0338 0.5645 0.4017 72 C 0.0182 0.7061 0.2758 73 E 0.0253 0.7131 0.2615 74 K 0.0240 0.7277 0.2482 75 R 0.0379 0.6547 0.3074 76 S 0.0428 0.6578 0.2994 77 I 0.0407 0.6236 0.3357 78 N 0.0528 0.4566 0.4906 79 L 0.0826 0.2558 0.6615 80 D 0.0759 0.1678 0.7564 81 E 0.0072 0.8634 0.1293 82 N 0.0054 0.9198 0.0748 83 D 0.0054 0.9382 0.0565 84 F 0.0047 0.9536 0.0417 85 L 0.0053 0.9559 0.0388 86 K 0.0047 0.9556 0.0397 87 L 0.0047 0.9538 0.0416 88 L 0.0047 0.9522 0.0431 89 L 0.0047 0.9408 0.0545 90 E 0.0048 0.9257 0.0695 91 F 0.0082 0.8851 0.1067 92 N 0.0208 0.7654 0.2138 93 K 0.0183 0.6941 0.2875 94 K 0.0476 0.3087 0.6437 95 G 0.0684 0.0645 0.8671 96 I 0.3265 0.0251 0.6484 97 H 0.5455 0.0329 0.4216 98 F 0.5810 0.0265 0.3925 99 F 0.3174 0.0233 0.6593