# This file is the result of combining several RDB files, specifically # T0358.t06.dssp-ebghstl.rdb (weight 1.53986) # T0358.t06.stride-ebghtl.rdb (weight 1.24869) # T0358.t06.str2.rdb (weight 1.54758) # T0358.t06.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 T0358.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # 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 T0358.t06-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 5.04225 # # ============================================ # Comments from T0358.t06.stride-ebghtl.rdb # ============================================ # TARGET T0358 # Using neural net t06-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 T0358.t06-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 5.04225 # # ============================================ # Comments from T0358.t06.str2.rdb # ============================================ # TARGET T0358 # Using neural net t06-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 T0358.t06-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 5.04225 # # ============================================ # Comments from T0358.t06.alpha.rdb # ============================================ # TARGET T0358 # Using neural net t06-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 T0358.t06-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 5.04225 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0693 0.0515 0.8791 2 T 0.1408 0.0835 0.7758 3 Q 0.2239 0.1264 0.6497 4 S 0.3425 0.1277 0.5298 5 V 0.4967 0.0764 0.4269 6 L 0.4919 0.0393 0.4688 7 L 0.2003 0.0191 0.7806 8 P 0.0941 0.0216 0.8844 9 P 0.0541 0.0872 0.8587 10 G 0.0873 0.0668 0.8459 11 P 0.1190 0.1286 0.7525 12 F 0.1809 0.1416 0.6775 13 T 0.1962 0.1972 0.6066 14 R 0.0216 0.8651 0.1133 15 R 0.0305 0.8570 0.1126 16 Q 0.0482 0.8263 0.1254 17 A 0.0802 0.8077 0.1121 18 Q 0.1390 0.7511 0.1098 19 A 0.2513 0.6555 0.0932 20 V 0.3167 0.5815 0.1017 21 T 0.3791 0.4836 0.1374 22 T 0.4029 0.3785 0.2186 23 T 0.4102 0.2227 0.3671 24 Y 0.4712 0.1528 0.3760 25 S 0.4108 0.1200 0.4692 26 N 0.3914 0.0754 0.5332 27 I 0.5912 0.0253 0.3836 28 T 0.7320 0.0167 0.2514 29 L 0.7201 0.0259 0.2540 30 E 0.5317 0.0464 0.4219 31 D 0.2477 0.0379 0.7144 32 D 0.0949 0.0836 0.8215 33 Q 0.0624 0.1071 0.8305 34 G 0.0804 0.1157 0.8039 35 S 0.2119 0.1137 0.6744 36 H 0.5870 0.0445 0.3685 37 F 0.8097 0.0209 0.1694 38 R 0.8776 0.0149 0.1075 39 L 0.9165 0.0089 0.0746 40 V 0.9217 0.0083 0.0700 41 V 0.9149 0.0073 0.0778 42 R 0.8697 0.0106 0.1197 43 D 0.4435 0.0203 0.5363 44 T 0.0484 0.1324 0.8192 45 E 0.0483 0.0377 0.9140 46 G 0.0658 0.0356 0.8986 47 R 0.3538 0.0273 0.6189 48 M 0.8520 0.0061 0.1419 49 V 0.8869 0.0109 0.1022 50 W 0.9009 0.0115 0.0876 51 R 0.8454 0.0260 0.1286 52 A 0.7312 0.0531 0.2157 53 W 0.4302 0.1037 0.4661 54 N 0.2617 0.0727 0.6655 55 F 0.1516 0.0659 0.7825 56 E 0.0983 0.0430 0.8586 57 P 0.0518 0.1584 0.7898 58 D 0.0474 0.1741 0.7785 59 A 0.0491 0.4445 0.5064 60 G 0.0307 0.4948 0.4745 61 E 0.0235 0.7126 0.2639 62 G 0.0318 0.7448 0.2234 63 L 0.0278 0.8046 0.1677 64 N 0.0232 0.8327 0.1442 65 R 0.0127 0.8961 0.0912 66 Y 0.0196 0.8897 0.0907 67 I 0.0304 0.8717 0.0979 68 R 0.0398 0.8064 0.1538 69 T 0.0291 0.7211 0.2497 70 S 0.0486 0.3888 0.5627 71 G 0.0576 0.1462 0.7961 72 I 0.2006 0.1082 0.6912 73 R 0.2660 0.1079 0.6261 74 T 0.1937 0.1708 0.6356 75 D 0.1548 0.1656 0.6796 76 T 0.1738 0.2027 0.6235 77 A 0.2325 0.1248 0.6428 78 T 0.1395 0.0771 0.7834 79 R 0.0490 0.0371 0.9139