# This file is the result of combining several RDB files, specifically # T0303.t04.dssp-ebghstl.rdb (weight 1.53986) # T0303.t04.stride-ebghtl.rdb (weight 1.24869) # T0303.t04.str2.rdb (weight 1.54758) # T0303.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 T0303.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.str2.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ # Comments from T0303.t04.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 29.889 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.0612 0.0620 0.8768 2 S 0.0808 0.1682 0.7509 3 L 0.0352 0.6071 0.3577 4 P 0.0134 0.8575 0.1291 5 D 0.0096 0.9187 0.0717 6 L 0.0047 0.9576 0.0377 7 A 0.0047 0.9597 0.0356 8 L 0.0047 0.9605 0.0349 9 S 0.0047 0.9606 0.0348 10 I 0.0047 0.9593 0.0360 11 N 0.0047 0.9597 0.0356 12 S 0.0047 0.9582 0.0372 13 A 0.0047 0.9570 0.0383 14 L 0.0048 0.9550 0.0402 15 K 0.0051 0.9432 0.0517 16 D 0.0062 0.8905 0.1033 17 V 0.0442 0.5009 0.4549 18 N 0.0315 0.0623 0.9062 19 L 0.0531 0.0157 0.9312 20 P 0.0676 0.0291 0.9034 21 Q 0.0852 0.0609 0.8539 22 A 0.0907 0.0321 0.8772 23 S 0.0703 0.0302 0.8995 24 E 0.0051 0.9284 0.0665 25 N 0.0056 0.9318 0.0625 26 L 0.0132 0.9174 0.0694 27 V 0.0272 0.9013 0.0715 28 M 0.0493 0.8734 0.0772 29 T 0.0517 0.8431 0.1052 30 W 0.0710 0.7850 0.1440 31 I 0.1042 0.6108 0.2850 32 G 0.0709 0.3718 0.5573 33 N 0.0376 0.4522 0.5102 34 G 0.0332 0.6539 0.3129 35 A 0.0076 0.8850 0.1073 36 D 0.0057 0.9138 0.0805 37 V 0.0104 0.9475 0.0421 38 L 0.0130 0.9466 0.0404 39 S 0.0128 0.9447 0.0425 40 Q 0.0123 0.9367 0.0510 41 R 0.0125 0.9231 0.0644 42 A 0.0118 0.8972 0.0910 43 V 0.0179 0.8506 0.1315 44 D 0.0203 0.7950 0.1847 45 W 0.0192 0.7602 0.2206 46 A 0.0236 0.6491 0.3273 47 C 0.0457 0.5152 0.4391 48 T 0.0649 0.4825 0.4526 49 Q 0.0829 0.4757 0.4414 50 A 0.0730 0.4522 0.4748 51 E 0.0661 0.3221 0.6119 52 K 0.0817 0.2744 0.6439 53 E 0.1097 0.1950 0.6954 54 L 0.1139 0.0575 0.8286 55 T 0.0572 0.0248 0.9180 56 E 0.0050 0.9337 0.0614 57 D 0.0048 0.9459 0.0493 58 E 0.0049 0.9496 0.0455 59 F 0.0047 0.9558 0.0394 60 K 0.0048 0.9559 0.0394 61 Y 0.0049 0.9479 0.0472 62 F 0.0049 0.9446 0.0505 63 K 0.0049 0.9506 0.0445 64 R 0.0053 0.9465 0.0482 65 Q 0.0057 0.9367 0.0577 66 F 0.0069 0.9342 0.0589 67 G 0.0058 0.9301 0.0641 68 F 0.0063 0.9257 0.0680 69 Y 0.0074 0.9228 0.0698 70 Y 0.0112 0.8969 0.0919 71 G 0.0099 0.8733 0.1168 72 E 0.0128 0.8190 0.1682 73 N 0.0260 0.7244 0.2496 74 L 0.0320 0.6968 0.2712 75 C 0.0504 0.5945 0.3550 76 N 0.0648 0.5541 0.3811 77 I 0.0876 0.4325 0.4799 78 S 0.0984 0.1846 0.7171 79 R 0.0577 0.1168 0.8255