# This file is the result of combining several RDB files, specifically # T0302.t06.dssp-ebghstl.rdb (weight 1.53986) # T0302.t06.stride-ebghtl.rdb (weight 1.24869) # T0302.t06.str2.rdb (weight 1.54758) # T0302.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 T0302.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t06.stride-ebghtl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t06.str2.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t06.alpha.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0647 0.0381 0.8971 2 M 0.1094 0.0254 0.8652 3 V 0.1363 0.0168 0.8469 4 S 0.0800 0.0135 0.9064 5 P 0.0259 0.6105 0.3636 6 E 0.0207 0.7402 0.2390 7 E 0.0365 0.7531 0.2104 8 A 0.0733 0.6879 0.2388 9 V 0.0735 0.6446 0.2819 10 K 0.0857 0.4786 0.4357 11 W 0.0653 0.2889 0.6457 12 G 0.0802 0.1580 0.7617 13 E 0.0904 0.1322 0.7774 14 S 0.1032 0.1405 0.7564 15 F 0.0052 0.9394 0.0553 16 D 0.0047 0.9551 0.0401 17 K 0.0048 0.9535 0.0417 18 L 0.0049 0.9431 0.0519 19 L 0.0064 0.8394 0.1542 20 S 0.0156 0.4736 0.5108 21 H 0.0658 0.0654 0.8688 22 R 0.0068 0.7701 0.2232 23 D 0.0111 0.7823 0.2065 24 G 0.0070 0.9028 0.0902 25 L 0.0048 0.9541 0.0412 26 E 0.0047 0.9591 0.0362 27 A 0.0047 0.9598 0.0355 28 F 0.0047 0.9603 0.0350 29 T 0.0047 0.9606 0.0347 30 R 0.0047 0.9594 0.0359 31 F 0.0047 0.9526 0.0426 32 L 0.0049 0.9252 0.0699 33 K 0.0057 0.8266 0.1677 34 T 0.0100 0.6727 0.3173 35 E 0.0220 0.4944 0.4836 36 F 0.0255 0.3495 0.6250 37 S 0.0302 0.3104 0.6594 38 E 0.0078 0.8728 0.1194 39 E 0.0075 0.8862 0.1063 40 N 0.0085 0.9098 0.0817 41 I 0.0135 0.9239 0.0627 42 E 0.0100 0.9409 0.0491 43 F 0.0189 0.9347 0.0465 44 W 0.0239 0.9340 0.0421 45 I 0.0198 0.9356 0.0446 46 A 0.0205 0.9128 0.0667 47 C 0.0076 0.9197 0.0727 48 E 0.0083 0.9121 0.0796 49 D 0.0149 0.8301 0.1551 50 F 0.0213 0.7492 0.2296 51 K 0.0466 0.5771 0.3763 52 K 0.0495 0.3986 0.5520 53 S 0.0631 0.2030 0.7339 54 K 0.0473 0.1310 0.8217 55 G 0.0564 0.0385 0.9051 56 P 0.0093 0.8334 0.1573 57 Q 0.0086 0.9117 0.0797 58 Q 0.0081 0.9322 0.0597 59 I 0.0060 0.9437 0.0502 60 H 0.0051 0.9524 0.0425 61 L 0.0047 0.9574 0.0379 62 K 0.0047 0.9571 0.0382 63 A 0.0047 0.9598 0.0355 64 K 0.0047 0.9602 0.0351 65 A 0.0047 0.9587 0.0366 66 I 0.0047 0.9558 0.0395 67 Y 0.0048 0.9549 0.0404 68 E 0.0055 0.9453 0.0492 69 K 0.0086 0.8959 0.0955 70 F 0.0121 0.7861 0.2018 71 I 0.0593 0.5653 0.3754 72 Q 0.0550 0.1660 0.7790 73 T 0.0274 0.2024 0.7702 74 D 0.0267 0.0886 0.8847 75 A 0.0798 0.0356 0.8846 76 P 0.1161 0.0575 0.8263 77 K 0.2438 0.0736 0.6827 78 E 0.4011 0.0722 0.5267 79 V 0.5034 0.0427 0.4539 80 N 0.3183 0.0205 0.6612 81 L 0.1064 0.0359 0.8577 82 D 0.0781 0.0550 0.8669 83 F 0.0061 0.8587 0.1351 84 H 0.0063 0.9039 0.0898 85 T 0.0058 0.9390 0.0551 86 K 0.0047 0.9563 0.0390 87 E 0.0047 0.9589 0.0364 88 V 0.0048 0.9568 0.0384 89 I 0.0056 0.9508 0.0437 90 T 0.0070 0.9339 0.0591 91 N 0.0093 0.8625 0.1282 92 S 0.0158 0.6996 0.2846 93 I 0.0532 0.4006 0.5462 94 T 0.0413 0.1725 0.7862 95 Q 0.0603 0.0584 0.8813 96 P 0.0687 0.0679 0.8634 97 T 0.0741 0.0852 0.8406 98 L 0.0197 0.7213 0.2590 99 H 0.0172 0.7347 0.2481 100 S 0.0236 0.7644 0.2120 101 F 0.0121 0.8865 0.1015 102 D 0.0068 0.9471 0.0461 103 A 0.0047 0.9568 0.0385 104 A 0.0047 0.9585 0.0367 105 Q 0.0047 0.9598 0.0355 106 S 0.0047 0.9602 0.0352 107 R 0.0047 0.9590 0.0363 108 V 0.0047 0.9587 0.0366 109 Y 0.0047 0.9595 0.0359 110 Q 0.0048 0.9568 0.0384 111 L 0.0050 0.9483 0.0467 112 M 0.0056 0.9164 0.0781 113 E 0.0081 0.7887 0.2032 114 Q 0.0178 0.6218 0.3604 115 D 0.0373 0.3735 0.5891 116 S 0.0363 0.3944 0.5693 117 Y 0.0468 0.4673 0.4859 118 T 0.0210 0.7158 0.2632 119 R 0.0238 0.7780 0.1981 120 F 0.0229 0.7651 0.2120 121 L 0.0483 0.6255 0.3261 122 K 0.0393 0.4829 0.4777 123 S 0.0595 0.3589 0.5816 124 D 0.0050 0.9087 0.0863 125 I 0.0054 0.9255 0.0692 126 Y 0.0053 0.9453 0.0494 127 L 0.0054 0.9473 0.0473 128 D 0.0071 0.9221 0.0708 129 L 0.0085 0.8719 0.1196 130 M 0.0208 0.7460 0.2332 131 E 0.0270 0.4888 0.4842 132 G 0.0311 0.0649 0.9040