# This file is the result of combining several RDB files, specifically # T0312.t04.dssp-ebghstl.rdb (weight 1.53986) # T0312.t04.stride-ebghtl.rdb (weight 1.24869) # T0312.t04.str2.rdb (weight 1.54758) # T0312.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 T0312.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0312 # 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 T0312.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 135 # # ============================================ # Comments from T0312.t04.stride-ebghtl.rdb # ============================================ # TARGET T0312 # 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 T0312.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 135 # # ============================================ # Comments from T0312.t04.str2.rdb # ============================================ # TARGET T0312 # 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 T0312.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 135 # # ============================================ # Comments from T0312.t04.alpha.rdb # ============================================ # TARGET T0312 # 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 T0312.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 135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1208 0.0102 0.8690 2 K 0.5361 0.0121 0.4518 3 V 0.6657 0.0202 0.3142 4 F 0.7091 0.0222 0.2686 5 E 0.7195 0.0270 0.2535 6 F 0.5247 0.0325 0.4428 7 E 0.3501 0.0481 0.6017 8 V 0.2236 0.0676 0.7088 9 G 0.1780 0.0415 0.7805 10 K 0.4069 0.0252 0.5679 11 G 0.7296 0.0058 0.2646 12 F 0.8762 0.0042 0.1196 13 L 0.9176 0.0033 0.0791 14 L 0.9132 0.0043 0.0825 15 R 0.9030 0.0035 0.0935 16 L 0.6918 0.0111 0.2971 17 D 0.2218 0.0139 0.7643 18 Y 0.0316 0.1337 0.8347 19 G 0.0342 0.1476 0.8182 20 K 0.0301 0.4177 0.5521 21 D 0.0670 0.6710 0.2620 22 L 0.0078 0.9180 0.0742 23 V 0.0055 0.9536 0.0409 24 R 0.0049 0.9578 0.0373 25 Q 0.0047 0.9595 0.0358 26 I 0.0047 0.9601 0.0353 27 E 0.0046 0.9613 0.0340 28 E 0.0046 0.9618 0.0336 29 F 0.0046 0.9616 0.0338 30 L 0.0047 0.9586 0.0367 31 E 0.0049 0.9474 0.0477 32 E 0.0065 0.8917 0.1018 33 K 0.0435 0.3961 0.5604 34 G 0.0465 0.0193 0.9341 35 I 0.0993 0.0102 0.8905 36 H 0.2653 0.0477 0.6871 37 A 0.8272 0.0074 0.1654 38 A 0.8948 0.0038 0.1014 39 H 0.9274 0.0044 0.0682 40 I 0.9207 0.0045 0.0748 41 S 0.8852 0.0103 0.1045 42 A 0.8501 0.0109 0.1391 43 I 0.7351 0.0528 0.2120 44 G 0.6630 0.0597 0.2773 45 A 0.6190 0.0505 0.3306 46 V 0.5636 0.0549 0.3815 47 R 0.5362 0.0709 0.3929 48 S 0.6607 0.0380 0.3013 49 A 0.8064 0.0147 0.1789 50 V 0.9017 0.0066 0.0917 51 I 0.8881 0.0109 0.1010 52 G 0.8136 0.0163 0.1701 53 Y 0.6644 0.0173 0.3183 54 Y 0.3261 0.0391 0.6347 55 D 0.1793 0.0415 0.7792 56 Q 0.0511 0.2837 0.6653 57 E 0.0595 0.3043 0.6363 58 K 0.0845 0.3244 0.5911 59 K 0.1104 0.3443 0.5453 60 E 0.2093 0.3773 0.4134 61 Y 0.3116 0.3434 0.3451 62 V 0.4673 0.2353 0.2974 63 K 0.5631 0.2208 0.2162 64 K 0.5818 0.1839 0.2344 65 E 0.5584 0.1657 0.2759 66 L 0.4503 0.1202 0.4294 67 M 0.2686 0.1056 0.6258 68 E 0.1887 0.0667 0.7447 69 P 0.2577 0.1125 0.6298 70 L 0.6725 0.0664 0.2611 71 E 0.8431 0.0340 0.1229 72 I 0.8858 0.0298 0.0844 73 L 0.8857 0.0223 0.0920 74 S 0.8866 0.0162 0.0972 75 L 0.8400 0.0245 0.1355 76 S 0.7668 0.0218 0.2114 77 G 0.6964 0.0211 0.2824 78 N 0.7211 0.0181 0.2608 79 V 0.7371 0.0194 0.2435 80 S 0.6124 0.0149 0.3727 81 M 0.2383 0.0680 0.6937 82 K 0.0779 0.0791 0.8430 83 D 0.0617 0.0548 0.8835 84 S 0.0509 0.0481 0.9010 85 K 0.1330 0.0182 0.8487 86 P 0.3816 0.0195 0.5989 87 F 0.6103 0.0272 0.3625 88 C 0.8114 0.0105 0.1781 89 H 0.8786 0.0065 0.1149 90 I 0.8943 0.0053 0.1004 91 H 0.9097 0.0054 0.0849 92 V 0.9115 0.0058 0.0827 93 L 0.9080 0.0070 0.0850 94 L 0.8584 0.0138 0.1278 95 G 0.6268 0.0226 0.3506 96 K 0.2801 0.0517 0.6682 97 D 0.0576 0.0521 0.8903 98 G 0.0797 0.0406 0.8797 99 E 0.5177 0.0200 0.4623 100 V 0.8254 0.0073 0.1673 101 Y 0.7887 0.0209 0.1904 102 G 0.7101 0.0231 0.2669 103 G 0.6295 0.0386 0.3318 104 H 0.6407 0.0360 0.3234 105 L 0.5514 0.0646 0.3840 106 F 0.3623 0.0617 0.5760 107 S 0.2227 0.0961 0.6812 108 A 0.2356 0.0764 0.6880 109 E 0.5214 0.0434 0.4352 110 V 0.6409 0.0276 0.3316 111 F 0.6055 0.0161 0.3783 112 A 0.6921 0.0094 0.2985 113 C 0.8306 0.0066 0.1628 114 E 0.9060 0.0034 0.0905 115 V 0.9209 0.0040 0.0751 116 F 0.9237 0.0034 0.0729 117 V 0.9116 0.0048 0.0836 118 L 0.8270 0.0120 0.1610 119 P 0.7018 0.0119 0.2863 120 L 0.2856 0.0536 0.6608 121 S 0.1006 0.0748 0.8246 122 G 0.0407 0.0812 0.8781 123 E 0.0811 0.0869 0.8320 124 A 0.1049 0.0777 0.8174 125 P 0.1268 0.2028 0.6704 126 E 0.1576 0.2987 0.5437 127 R 0.2700 0.2121 0.5180 128 A 0.3261 0.1092 0.5647 129 F 0.3169 0.0703 0.6128 130 D 0.1417 0.0277 0.8307 131 E 0.0128 0.3932 0.5941 132 Q 0.0155 0.3194 0.6650 133 T 0.0639 0.2907 0.6454 134 G 0.0880 0.1115 0.8005 135 L 0.3024 0.0855 0.6121 136 F 0.5585 0.1014 0.3401 137 L 0.5807 0.1236 0.2958 138 W 0.4798 0.1115 0.4086 139 L 0.3620 0.1320 0.5060 140 E 0.2493 0.1430 0.6076 141 H 0.1573 0.1748 0.6679 142 H 0.1193 0.1354 0.7453 143 H 0.0778 0.1275 0.7948 144 H 0.0749 0.1057 0.8193 145 H 0.0738 0.0828 0.8434 146 H 0.0496 0.0391 0.9112