# This file is the result of combining several RDB files, specifically # T0230.t04.dssp-ebghstl.rdb (weight 1.53986) # T0230.t04.stride-ebghtl.rdb (weight 1.24869) # T0230.t04.str2.rdb (weight 1.54758) # T0230.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 T0230.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0230 # 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 T0230.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 48.2413 # # ============================================ # Comments from T0230.t04.stride-ebghtl.rdb # ============================================ # TARGET T0230 # 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 T0230.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 48.2413 # # ============================================ # Comments from T0230.t04.str2.rdb # ============================================ # TARGET T0230 # 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 T0230.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 48.2413 # # ============================================ # Comments from T0230.t04.alpha.rdb # ============================================ # TARGET T0230 # 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 T0230.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 48.2413 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0582 0.0141 0.9277 2 P 0.0655 0.0444 0.8901 3 M 0.0477 0.1787 0.7737 4 S 0.0493 0.2478 0.7030 5 K 0.0428 0.3296 0.6276 6 K 0.0664 0.2475 0.6861 7 V 0.1329 0.2246 0.6424 8 T 0.0831 0.2416 0.6754 9 K 0.0048 0.9473 0.0479 10 E 0.0047 0.9581 0.0372 11 D 0.0047 0.9579 0.0374 12 V 0.0048 0.9575 0.0378 13 L 0.0048 0.9563 0.0389 14 N 0.0050 0.9532 0.0418 15 A 0.0057 0.9396 0.0547 16 L 0.0067 0.9020 0.0914 17 K 0.0082 0.7743 0.2175 18 N 0.0127 0.5069 0.4805 19 V 0.0818 0.3119 0.6063 20 I 0.1223 0.2214 0.6563 21 D 0.1556 0.0637 0.7806 22 F 0.0477 0.2707 0.6816 23 E 0.0516 0.2882 0.6602 24 L 0.0837 0.2120 0.7042 25 G 0.0790 0.0556 0.8654 26 L 0.1375 0.0174 0.8451 27 D 0.2606 0.0219 0.7175 28 V 0.4116 0.3784 0.2100 29 V 0.4761 0.3595 0.1644 30 S 0.5400 0.2800 0.1800 31 L 0.4329 0.2532 0.3138 32 G 0.3367 0.1025 0.5608 33 L 0.6908 0.0325 0.2768 34 V 0.8443 0.0095 0.1462 35 Y 0.8043 0.0237 0.1720 36 D 0.8540 0.0061 0.1399 37 I 0.8514 0.0049 0.1437 38 Q 0.9003 0.0034 0.0963 39 I 0.8415 0.0061 0.1524 40 D 0.4930 0.0159 0.4911 41 D 0.0914 0.0999 0.8087 42 Q 0.0647 0.0687 0.8666 43 N 0.1126 0.0394 0.8480 44 N 0.4551 0.0121 0.5328 45 V 0.8912 0.0037 0.1051 46 K 0.9216 0.0035 0.0749 47 V 0.9254 0.0033 0.0713 48 L 0.9259 0.0035 0.0706 49 M 0.9145 0.0038 0.0817 50 T 0.8660 0.0058 0.1282 51 M 0.6270 0.0123 0.3607 52 T 0.2539 0.0344 0.7118 53 T 0.0979 0.0588 0.8432 54 P 0.0363 0.1635 0.8002 55 M 0.0474 0.1897 0.7629 56 C 0.0800 0.2774 0.6425 57 P 0.0338 0.5633 0.4029 58 L 0.0125 0.8007 0.1867 59 A 0.0079 0.8863 0.1058 60 G 0.0064 0.9068 0.0868 61 M 0.0070 0.9218 0.0712 62 I 0.0053 0.9280 0.0667 63 L 0.0049 0.9431 0.0520 64 S 0.0051 0.9402 0.0546 65 D 0.0053 0.9383 0.0564 66 A 0.0048 0.9526 0.0426 67 E 0.0048 0.9587 0.0365 68 E 0.0048 0.9587 0.0365 69 A 0.0049 0.9543 0.0408 70 I 0.0051 0.9315 0.0634 71 K 0.0062 0.8227 0.1711 72 K 0.0125 0.6112 0.3762 73 I 0.0750 0.2106 0.7144 74 E 0.0269 0.2373 0.7358 75 G 0.0400 0.1307 0.8294 76 V 0.2224 0.0951 0.6825 77 N 0.3030 0.0704 0.6266 78 N 0.6052 0.0281 0.3667 79 V 0.8420 0.0042 0.1538 80 E 0.9178 0.0034 0.0789 81 V 0.9237 0.0033 0.0729 82 E 0.9208 0.0034 0.0758 83 L 0.9088 0.0033 0.0879 84 T 0.8239 0.0054 0.1707 85 F 0.5950 0.0090 0.3961 86 D 0.1862 0.0187 0.7951 87 P 0.0802 0.0332 0.8866 88 P 0.0533 0.0676 0.8791 89 W 0.0976 0.0510 0.8514 90 T 0.0841 0.0446 0.8714 91 P 0.0176 0.5179 0.4646 92 E 0.0152 0.5625 0.4223 93 R 0.0382 0.5374 0.4244 94 M 0.1159 0.2413 0.6428 95 S 0.0579 0.1148 0.8274 96 P 0.0048 0.9358 0.0594 97 E 0.0047 0.9540 0.0413 98 L 0.0048 0.9573 0.0379 99 R 0.0047 0.9584 0.0369 100 E 0.0050 0.9476 0.0474 101 K 0.0067 0.9003 0.0930 102 F 0.0462 0.5096 0.4442 103 G 0.0328 0.0557 0.9115 104 V 0.0528 0.0272 0.9200