# This file is the result of combining several RDB files, specifically # T0190.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0190.t2k.stride-ebghtl.rdb (weight 1.24869) # T0190.t2k.str.rdb (weight 1.53983) # T0190.t2k.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 T0190.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0190 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0190.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 36 # # ============================================ # Comments from T0190.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0190 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0190.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 36 # # ============================================ # Comments from T0190.t2k.str.rdb # ============================================ # TARGET T0190 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0190.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 36 # # ============================================ # Comments from T0190.t2k.alpha.rdb # ============================================ # TARGET T0190 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0190.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 36 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0516 0.0488 0.8996 2 Q 0.0602 0.0785 0.8613 3 Q 0.0672 0.0753 0.8575 4 N 0.0965 0.0464 0.8572 5 I 0.1398 0.0802 0.7799 6 L 0.4197 0.0649 0.5154 7 S 0.6234 0.0368 0.3397 8 V 0.8015 0.0410 0.1575 9 H 0.8559 0.0321 0.1119 10 I 0.8453 0.0507 0.1041 11 L 0.7841 0.0592 0.1567 12 N 0.6243 0.0737 0.3020 13 Q 0.3156 0.1825 0.5019 14 Q 0.1883 0.1412 0.6704 15 T 0.1166 0.0862 0.7973 16 G 0.0943 0.0425 0.8632 17 K 0.2904 0.0336 0.6760 18 P 0.3478 0.0529 0.5993 19 A 0.1655 0.0968 0.7377 20 A 0.0822 0.1125 0.8053 21 D 0.1258 0.0387 0.8355 22 V 0.3565 0.0076 0.6359 23 T 0.7807 0.0038 0.2156 24 V 0.9024 0.0036 0.0940 25 T 0.9234 0.0038 0.0729 26 L 0.9225 0.0034 0.0742 27 E 0.9016 0.0045 0.0940 28 K 0.8738 0.0045 0.1217 29 K 0.5830 0.0123 0.4046 30 A 0.1620 0.0606 0.7774 31 D 0.0543 0.0322 0.9134 32 N 0.0619 0.0472 0.8908 33 G 0.4495 0.0295 0.5210 34 W 0.7246 0.0224 0.2530 35 L 0.7571 0.0205 0.2224 36 Q 0.8004 0.0263 0.1732 37 L 0.7664 0.0377 0.1959 38 N 0.7009 0.0505 0.2486 39 T 0.6509 0.0525 0.2966 40 A 0.6903 0.0251 0.2846 41 K 0.7051 0.0166 0.2783 42 T 0.6407 0.0154 0.3440 43 D 0.1178 0.0285 0.8536 44 K 0.0205 0.1217 0.8578 45 D 0.0543 0.0308 0.9149 46 G 0.0774 0.0353 0.8873 47 R 0.3205 0.0233 0.6562 48 I 0.5420 0.0251 0.4330 49 K 0.1974 0.0815 0.7212 50 A 0.1238 0.1430 0.7332 51 L 0.1372 0.1520 0.7108 52 W 0.1615 0.0813 0.7572 53 P 0.1182 0.0968 0.7850 54 E 0.0382 0.4960 0.4658 55 Q 0.0391 0.4994 0.4614 56 T 0.0898 0.4067 0.5035 57 A 0.2089 0.1165 0.6745 58 T 0.2507 0.0650 0.6843 59 T 0.3380 0.0589 0.6031 60 G 0.5030 0.0242 0.4729 61 D 0.7782 0.0067 0.2152 62 Y 0.8955 0.0041 0.1004 63 R 0.9196 0.0038 0.0766 64 V 0.9189 0.0041 0.0770 65 V 0.9044 0.0054 0.0902 66 F 0.8392 0.0103 0.1505 67 K 0.5968 0.0213 0.3819 68 T 0.1870 0.2752 0.5377 69 G 0.0179 0.7575 0.2246 70 D 0.0092 0.8713 0.1195 71 Y 0.0085 0.9099 0.0816 72 F 0.0095 0.9218 0.0687 73 K 0.0086 0.8944 0.0970 74 K 0.0088 0.7722 0.2190 75 Q 0.0446 0.2874 0.6681 76 N 0.0416 0.0254 0.9330 77 L 0.0764 0.0169 0.9066 78 E 0.0906 0.0280 0.8814 79 S 0.1296 0.1041 0.7663 80 F 0.2099 0.1390 0.6511 81 F 0.2909 0.1160 0.5931 82 P 0.3402 0.1165 0.5433 83 E 0.4556 0.0427 0.5017 84 I 0.6956 0.0072 0.2972 85 P 0.8613 0.0039 0.1348 86 V 0.8980 0.0036 0.0983 87 E 0.9180 0.0040 0.0781 88 F 0.9081 0.0049 0.0869 89 H 0.8783 0.0049 0.1168 90 I 0.7335 0.0159 0.2506 91 N 0.4195 0.0369 0.5436 92 K 0.1006 0.0717 0.8278 93 V 0.0279 0.1055 0.8666 94 N 0.0351 0.0703 0.8947 95 E 0.1868 0.0471 0.7661 96 H 0.5421 0.0188 0.4392 97 Y 0.8202 0.0103 0.1694 98 H 0.8613 0.0134 0.1252 99 V 0.8539 0.0191 0.1269 100 P 0.8100 0.0426 0.1474 101 L 0.7510 0.0908 0.1582 102 L 0.7683 0.0662 0.1655 103 L 0.5933 0.0705 0.3361 104 S 0.2552 0.0379 0.7069 105 Q 0.0831 0.1766 0.7404 106 Y 0.1063 0.1900 0.7037 107 G 0.1603 0.1992 0.6404 108 Y 0.2634 0.1660 0.5705 109 S 0.3345 0.1386 0.5268 110 T 0.3370 0.1424 0.5206 111 Y 0.3334 0.1114 0.5552 112 R 0.1914 0.1011 0.7075 113 G 0.0810 0.0647 0.8542 114 S 0.0463 0.0450 0.9088