# This file is the result of combining several RDB files, specifically # T0602.t04.dssp-ebghstl.rdb (weight 1.53986) # T0602.t04.stride-ebghtl.rdb (weight 1.24869) # T0602.t04.str2.rdb (weight 1.54758) # T0602.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 T0602.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0602 # 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 T0602.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 64.8643 # # ============================================ # Comments from T0602.t04.stride-ebghtl.rdb # ============================================ # TARGET T0602 # 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 T0602.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 64.8643 # # ============================================ # Comments from T0602.t04.str2.rdb # ============================================ # TARGET T0602 # 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 T0602.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 64.8643 # # ============================================ # Comments from T0602.t04.alpha.rdb # ============================================ # TARGET T0602 # 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 T0602.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 64.8643 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0463 0.2119 0.7418 2 N 0.0416 0.3226 0.6358 3 A 0.0350 0.3670 0.5979 4 M 0.0453 0.3350 0.6197 5 E 0.0342 0.3703 0.5955 6 R 0.0335 0.3703 0.5962 7 H 0.0140 0.6943 0.2917 8 Q 0.0065 0.9092 0.0843 9 H 0.0058 0.9221 0.0721 10 L 0.0051 0.9416 0.0533 11 L 0.0051 0.9498 0.0451 12 S 0.0048 0.9547 0.0405 13 E 0.0048 0.9540 0.0411 14 Y 0.0047 0.9590 0.0364 15 Q 0.0047 0.9607 0.0346 16 Q 0.0046 0.9614 0.0340 17 I 0.0047 0.9593 0.0360 18 L 0.0047 0.9567 0.0386 19 T 0.0047 0.9391 0.0562 20 L 0.0048 0.9233 0.0719 21 S 0.0052 0.9147 0.0801 22 E 0.0047 0.9594 0.0360 23 Q 0.0047 0.9608 0.0346 24 M 0.0047 0.9596 0.0357 25 L 0.0047 0.9594 0.0359 26 V 0.0046 0.9586 0.0368 27 L 0.0047 0.9543 0.0410 28 A 0.0049 0.9365 0.0586 29 T 0.0059 0.8585 0.1356 30 E 0.0445 0.4380 0.5175 31 G 0.0316 0.1125 0.8559 32 N 0.0793 0.0827 0.8380 33 W 0.0101 0.8509 0.1390 34 D 0.0050 0.9448 0.0502 35 A 0.0050 0.9529 0.0421 36 L 0.0047 0.9571 0.0381 37 V 0.0048 0.9570 0.0382 38 D 0.0048 0.9567 0.0385 39 L 0.0048 0.9545 0.0407 40 E 0.0048 0.9561 0.0391 41 M 0.0047 0.9597 0.0356 42 T 0.0047 0.9605 0.0348 43 Y 0.0047 0.9589 0.0364 44 L 0.0047 0.9603 0.0350 45 K 0.0046 0.9615 0.0339 46 A 0.0047 0.9596 0.0357 47 V 0.0047 0.9572 0.0381 48 E 0.0047 0.9525 0.0427 49 S 0.0050 0.9352 0.0599 50 T 0.0062 0.8921 0.1017 51 A 0.0130 0.7540 0.2330 52 N 0.0215 0.5355 0.4430 53 I 0.0609 0.3278 0.6113 54 T 0.0793 0.1762 0.7445 55 I 0.0736 0.2314 0.6950 56 S 0.0645 0.2326 0.7029 57 S 0.0515 0.2747 0.6738 58 C 0.0662 0.2065 0.7274 59 S 0.0632 0.1779 0.7589 60 S 0.0457 0.3383 0.6160 61 L 0.0049 0.9300 0.0651 62 M 0.0047 0.9487 0.0465 63 L 0.0047 0.9523 0.0429 64 Q 0.0047 0.9559 0.0394 65 D 0.0047 0.9548 0.0405 66 L 0.0047 0.9482 0.0472 67 L 0.0047 0.9458 0.0494 68 R 0.0047 0.9579 0.0375 69 E 0.0047 0.9598 0.0356 70 K 0.0046 0.9589 0.0365 71 L 0.0047 0.9596 0.0358 72 R 0.0047 0.9606 0.0347 73 A 0.0047 0.9563 0.0391 74 I 0.0047 0.9468 0.0485 75 L 0.0051 0.9226 0.0723 76 D 0.0071 0.8864 0.1066 77 N 0.0119 0.8071 0.1810 78 E 0.0052 0.9488 0.0460 79 I 0.0047 0.9572 0.0381 80 E 0.0047 0.9565 0.0388 81 I 0.0047 0.9569 0.0384 82 K 0.0047 0.9590 0.0363 83 R 0.0047 0.9555 0.0398 84 L 0.0047 0.9500 0.0453 85 L 0.0047 0.9442 0.0511 86 Q 0.0047 0.9346 0.0607 87 L 0.0047 0.9208 0.0745 88 R 0.0048 0.9020 0.0932 89 L 0.0047 0.9402 0.0550 90 D 0.0047 0.9437 0.0516 91 R 0.0048 0.9407 0.0545 92 L 0.0048 0.9492 0.0459 93 S 0.0048 0.9522 0.0430 94 D 0.0049 0.9465 0.0486 95 L 0.0056 0.9239 0.0706 96 V 0.0092 0.8102 0.1806 97 G 0.0119 0.5126 0.4756 98 Q 0.0216 0.4948 0.4836 99 S 0.0242 0.5019 0.4739 100 T 0.0200 0.6905 0.2894 101 K 0.0128 0.8605 0.1267 102 Q 0.0179 0.9065 0.0757 103 Q 0.0254 0.9057 0.0689 104 A 0.0242 0.9094 0.0665 105 V 0.0159 0.9230 0.0611 106 N 0.0216 0.8854 0.0929 107 N 0.0244 0.8156 0.1601 108 T 0.0306 0.7709 0.1984 109 Y 0.0516 0.5756 0.3728 110 G 0.0623 0.2582 0.6795 111 Q 0.0931 0.1815 0.7255 112 F 0.0926 0.0477 0.8597 113 P 0.0437 0.1312 0.8252 114 D 0.0392 0.1474 0.8134 115 H 0.1852 0.1272 0.6876 116 A 0.4720 0.0725 0.4554 117 L 0.6307 0.0464 0.3229 118 L 0.6019 0.0350 0.3631 119 L 0.3553 0.0767 0.5680 120 G 0.1585 0.0680 0.7735 121 E 0.1304 0.0917 0.7779 122 T 0.1099 0.0763 0.8138 123 Q 0.0632 0.0542 0.8826