# This file is the result of combining several RDB files, specifically # T0314.t06.dssp-ebghstl.rdb (weight 1.53986) # T0314.t06.stride-ebghtl.rdb (weight 1.24869) # T0314.t06.str2.rdb (weight 1.54758) # T0314.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 T0314.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t06.stride-ebghtl.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t06.str2.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ # Comments from T0314.t06.alpha.rdb # ============================================ # TARGET T0314 # 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 T0314.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 2.50627 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0939 0.0146 0.8914 2 S 0.3094 0.0279 0.6627 3 I 0.3232 0.0361 0.6407 4 T 0.2004 0.0459 0.7537 5 S 0.0526 0.6029 0.3445 6 T 0.0076 0.9177 0.0747 7 D 0.0085 0.9270 0.0645 8 I 0.0059 0.9380 0.0561 9 C 0.0069 0.9313 0.0618 10 Q 0.0071 0.9043 0.0886 11 A 0.0084 0.8635 0.1281 12 A 0.0122 0.8225 0.1653 13 D 0.0129 0.7135 0.2737 14 A 0.0146 0.6693 0.3160 15 L 0.0756 0.4865 0.4379 16 K 0.0667 0.3194 0.6139 17 G 0.1625 0.1988 0.6386 18 F 0.4383 0.1414 0.4202 19 V 0.6005 0.0961 0.3034 20 G 0.5820 0.0642 0.3538 21 F 0.5205 0.0775 0.4019 22 N 0.4143 0.0697 0.5159 23 R 0.1381 0.1456 0.7163 24 K 0.1780 0.1338 0.6882 25 T 0.1394 0.0603 0.8003 26 G 0.2206 0.0264 0.7529 27 R 0.5766 0.0108 0.4126 28 Y 0.8964 0.0037 0.0999 29 I 0.9173 0.0033 0.0794 30 V 0.9198 0.0037 0.0765 31 R 0.8894 0.0057 0.1049 32 F 0.6631 0.0116 0.3253 33 S 0.3332 0.0269 0.6399 34 E 0.1005 0.1775 0.7220 35 D 0.0669 0.2506 0.6825 36 S 0.0622 0.3741 0.5637 37 F 0.0930 0.1847 0.7223 38 G 0.1246 0.1141 0.7613 39 M 0.2020 0.0786 0.7194 40 D 0.2788 0.0869 0.6343 41 V 0.1310 0.3096 0.5594 42 A 0.1280 0.2724 0.5995 43 D 0.1146 0.2720 0.6133 44 D 0.0634 0.2249 0.7117 45 S 0.1158 0.1438 0.7404 46 I 0.2592 0.0666 0.6742 47 T 0.2306 0.0275 0.7420 48 P 0.2227 0.0354 0.7419 49 T 0.1652 0.1626 0.6722 50 S 0.1981 0.2341 0.5679 51 E 0.3630 0.2478 0.3893 52 F 0.6147 0.1099 0.2754 53 V 0.7392 0.0664 0.1944 54 W 0.7270 0.0465 0.2265 55 S 0.5536 0.0491 0.3973 56 S 0.3675 0.1156 0.5169 57 V 0.2001 0.1767 0.6232 58 R 0.1570 0.1558 0.6872 59 D 0.0874 0.2145 0.6981 60 D 0.1768 0.2360 0.5871 61 V 0.4736 0.2248 0.3016 62 M 0.5993 0.1571 0.2437 63 R 0.5251 0.1959 0.2790 64 L 0.3242 0.2526 0.4232 65 G 0.1603 0.2387 0.6010 66 R 0.0342 0.7996 0.1663 67 E 0.0303 0.8893 0.0804 68 Q 0.0220 0.9229 0.0551 69 L 0.0200 0.9289 0.0511 70 Q 0.0156 0.9384 0.0460 71 I 0.0146 0.9416 0.0438 72 L 0.0184 0.9238 0.0578 73 L 0.0220 0.8807 0.0973 74 E 0.0252 0.7806 0.1942 75 Q 0.0632 0.5115 0.4253 76 N 0.0803 0.1893 0.7303 77 I 0.0633 0.3433 0.5934 78 N 0.0601 0.3446 0.5953 79 E 0.0688 0.4636 0.4676 80 R 0.1356 0.4199 0.4445 81 L 0.2541 0.2776 0.4683 82 N 0.2015 0.1128 0.6857 83 I 0.0797 0.1416 0.7787 84 G 0.0500 0.1111 0.8389 85 E 0.0962 0.0938 0.8100 86 P 0.2211 0.1601 0.6188 87 L 0.4314 0.2157 0.3528 88 L 0.6859 0.1703 0.1438 89 V 0.7664 0.1311 0.1024 90 Y 0.7384 0.1395 0.1221 91 L 0.6530 0.1260 0.2210 92 R 0.4399 0.1130 0.4471 93 R 0.1416 0.3243 0.5341 94 Q 0.0624 0.2759 0.6617 95 D 0.0551 0.2361 0.7088 96 L 0.0849 0.0986 0.8165 97 P 0.0883 0.1872 0.7245 98 E 0.3226 0.3383 0.3391 99 I 0.5245 0.2828 0.1927 100 T 0.6039 0.2284 0.1676 101 A 0.6018 0.2151 0.1831 102 Q 0.5544 0.2287 0.2169 103 R 0.4544 0.2224 0.3232 104 Q 0.3293 0.1934 0.4772 105 L 0.1482 0.1752 0.6766 106 R 0.0442 0.0557 0.9002