# This file is the result of combining several RDB files, specifically # T0277.t04.dssp-ebghstl.rdb (weight 1.53986) # T0277.t04.stride-ebghtl.rdb (weight 1.24869) # T0277.t04.str2.rdb (weight 1.54758) # T0277.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 T0277.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0277 # Using neural net t04-2621-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 T0277.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 12.5384 # # ============================================ # Comments from T0277.t04.stride-ebghtl.rdb # ============================================ # TARGET T0277 # 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 T0277.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 12.5384 # # ============================================ # Comments from T0277.t04.str2.rdb # ============================================ # TARGET T0277 # 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 T0277.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 12.5384 # # ============================================ # Comments from T0277.t04.alpha.rdb # ============================================ # TARGET T0277 # 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 T0277.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 12.5384 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0177 0.3092 0.6731 2 A 0.0148 0.6569 0.3283 3 S 0.0135 0.7832 0.2034 4 L 0.0047 0.9494 0.0459 5 A 0.0047 0.9605 0.0348 6 R 0.0047 0.9606 0.0347 7 A 0.0047 0.9603 0.0350 8 V 0.0047 0.9611 0.0342 9 E 0.0046 0.9614 0.0340 10 R 0.0046 0.9604 0.0350 11 L 0.0047 0.9563 0.0389 12 K 0.0048 0.9508 0.0444 13 A 0.0054 0.9152 0.0794 14 A 0.0083 0.8489 0.1428 15 L 0.0203 0.7001 0.2797 16 E 0.0304 0.3751 0.5945 17 R 0.0520 0.0666 0.8814 18 P 0.0439 0.0484 0.9077 19 K 0.0305 0.3693 0.6002 20 D 0.0286 0.6601 0.3113 21 E 0.0277 0.8293 0.1430 22 F 0.0257 0.8856 0.0887 23 I 0.0245 0.9040 0.0715 24 R 0.0246 0.9082 0.0671 25 D 0.0186 0.9101 0.0714 26 S 0.0279 0.8827 0.0894 27 A 0.0571 0.8433 0.0996 28 I 0.0894 0.8163 0.0943 29 Q 0.0465 0.8356 0.1179 30 R 0.0322 0.8091 0.1588 31 F 0.0504 0.7803 0.1693 32 E 0.0457 0.8372 0.1172 33 F 0.0346 0.9007 0.0646 34 T 0.0147 0.9342 0.0511 35 F 0.0059 0.9547 0.0394 36 E 0.0049 0.9601 0.0349 37 L 0.0051 0.9597 0.0352 38 A 0.0047 0.9588 0.0365 39 W 0.0047 0.9576 0.0377 40 K 0.0046 0.9608 0.0345 41 T 0.0047 0.9604 0.0350 42 L 0.0047 0.9589 0.0364 43 K 0.0047 0.9609 0.0345 44 T 0.0047 0.9603 0.0350 45 F 0.0048 0.9570 0.0382 46 L 0.0048 0.9518 0.0433 47 E 0.0053 0.9334 0.0613 48 L 0.0098 0.9007 0.0894 49 Q 0.0419 0.4713 0.4867 50 G 0.0359 0.0466 0.9174 51 L 0.0994 0.0417 0.8589 52 E 0.2543 0.0724 0.6733 53 A 0.2241 0.1257 0.6502 54 R 0.1382 0.1161 0.7457 55 S 0.0876 0.0522 0.8602 56 P 0.0259 0.7389 0.2352 57 R 0.0092 0.9142 0.0765 58 A 0.0086 0.9419 0.0495 59 A 0.0064 0.9524 0.0412 60 I 0.0068 0.9516 0.0416 61 R 0.0056 0.9525 0.0419 62 G 0.0064 0.9457 0.0479 63 A 0.0065 0.9374 0.0561 64 F 0.0122 0.9134 0.0744 65 Q 0.0208 0.8727 0.1065 66 V 0.0556 0.6187 0.3257 67 G 0.0444 0.2791 0.6765 68 L 0.1072 0.1008 0.7920 69 L 0.1193 0.0366 0.8440 70 P 0.0798 0.0555 0.8648 71 E 0.0414 0.1979 0.7607 72 D 0.0427 0.5622 0.3951 73 P 0.0149 0.8688 0.1162 74 F 0.0170 0.9114 0.0716 75 W 0.0164 0.9350 0.0487 76 L 0.0138 0.9421 0.0441 77 E 0.0179 0.9296 0.0524 78 M 0.0152 0.9201 0.0647 79 L 0.0129 0.9144 0.0728 80 E 0.0193 0.8582 0.1225 81 L 0.0330 0.7770 0.1900 82 R 0.0591 0.5612 0.3798 83 N 0.0692 0.2538 0.6770 84 L 0.0765 0.2897 0.6337 85 T 0.1112 0.2572 0.6316 86 N 0.1039 0.2550 0.6411 87 H 0.1083 0.2519 0.6397 88 T 0.1226 0.2989 0.5784 89 Y 0.1113 0.2215 0.6672 90 D 0.0583 0.1956 0.7461 91 E 0.0051 0.9525 0.0424 92 A 0.0047 0.9585 0.0368 93 L 0.0047 0.9592 0.0361 94 A 0.0047 0.9608 0.0346 95 E 0.0047 0.9605 0.0349 96 R 0.0048 0.9585 0.0367 97 I 0.0049 0.9527 0.0425 98 Y 0.0050 0.9418 0.0532 99 A 0.0066 0.9035 0.0899 100 E 0.0104 0.7990 0.1906 101 L 0.0362 0.5052 0.4586 102 P 0.0083 0.6990 0.2927 103 K 0.0061 0.7833 0.2106 104 A 0.0059 0.8341 0.1600 105 L 0.0051 0.9182 0.0767 106 E 0.0049 0.9449 0.0503 107 R 0.0048 0.9442 0.0510 108 F 0.0048 0.9531 0.0421 109 Q 0.0047 0.9589 0.0364 110 E 0.0047 0.9594 0.0359 111 L 0.0047 0.9563 0.0389 112 L 0.0048 0.9505 0.0447 113 R 0.0053 0.9306 0.0641 114 R 0.0071 0.8835 0.1094 115 L 0.0318 0.7385 0.2297 116 E 0.0417 0.2473 0.7110 117 E 0.0535 0.0693 0.8772 118 P 0.0434 0.0382 0.9185 119 A 0.0370 0.0474 0.9157