# This file is the result of combining several RDB files, specifically # T0364.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0364.t2k.stride-ebghtl.rdb (weight 1.24869) # T0364.t2k.str2.rdb (weight 1.54758) # T0364.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 T0364.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0364 # 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 T0364.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 151 # # ============================================ # Comments from T0364.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0364 # 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 T0364.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 151 # # ============================================ # Comments from T0364.t2k.str2.rdb # ============================================ # TARGET T0364 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0364.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 151 # # ============================================ # Comments from T0364.t2k.alpha.rdb # ============================================ # TARGET T0364 # 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 T0364.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 151 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0733 0.0351 0.8916 2 P 0.0956 0.0347 0.8696 3 A 0.1608 0.0344 0.8048 4 L 0.2439 0.0334 0.7227 5 I 0.5839 0.0185 0.3976 6 T 0.7843 0.0114 0.2043 7 Y 0.7889 0.0088 0.2023 8 R 0.7805 0.0130 0.2066 9 T 0.7316 0.0088 0.2596 10 T 0.7369 0.0064 0.2566 11 V 0.5510 0.0089 0.4401 12 Q 0.2102 0.0122 0.7776 13 E 0.0365 0.5300 0.4335 14 D 0.0227 0.6256 0.3517 15 W 0.0523 0.6731 0.2746 16 V 0.1270 0.5544 0.3186 17 D 0.1208 0.4611 0.4181 18 Y 0.0343 0.4970 0.4687 19 N 0.0496 0.3276 0.6228 20 G 0.0729 0.2880 0.6391 21 H 0.1395 0.3387 0.5218 22 L 0.1833 0.4428 0.3739 23 R 0.1002 0.5251 0.3747 24 D 0.0399 0.7100 0.2501 25 A 0.0239 0.8298 0.1463 26 F 0.0241 0.8818 0.0941 27 Y 0.0133 0.9327 0.0540 28 L 0.0078 0.9479 0.0443 29 L 0.0073 0.9475 0.0452 30 I 0.0057 0.9479 0.0465 31 F 0.0048 0.9518 0.0434 32 S 0.0050 0.9512 0.0438 33 Y 0.0051 0.9477 0.0472 34 A 0.0051 0.9487 0.0462 35 T 0.0048 0.9547 0.0405 36 D 0.0048 0.9552 0.0400 37 A 0.0047 0.9535 0.0418 38 L 0.0047 0.9542 0.0411 39 M 0.0049 0.9484 0.0467 40 D 0.0054 0.9341 0.0605 41 R 0.0076 0.8613 0.1312 42 I 0.0436 0.4397 0.5167 43 G 0.0418 0.0454 0.9129 44 L 0.0772 0.0202 0.9026 45 D 0.0683 0.0170 0.9147 46 A 0.0089 0.8969 0.0942 47 D 0.0052 0.9369 0.0579 48 S 0.0054 0.9462 0.0484 49 R 0.0060 0.9482 0.0459 50 G 0.0071 0.9226 0.0703 51 Q 0.0080 0.8435 0.1485 52 S 0.0418 0.4496 0.5087 53 G 0.0331 0.0790 0.8880 54 N 0.0805 0.0680 0.8515 55 S 0.1990 0.0889 0.7122 56 L 0.4438 0.2522 0.3040 57 F 0.5416 0.2854 0.1730 58 T 0.5921 0.2714 0.1365 59 L 0.5414 0.3311 0.1274 60 E 0.4945 0.3656 0.1399 61 A 0.4328 0.4268 0.1404 62 H 0.4143 0.4364 0.1493 63 I 0.4340 0.4064 0.1596 64 N 0.3932 0.4031 0.2037 65 Y 0.3902 0.3588 0.2510 66 L 0.3992 0.2788 0.3220 67 H 0.3683 0.2005 0.4312 68 E 0.4178 0.1313 0.4510 69 V 0.3667 0.0522 0.5810 70 K 0.1812 0.0359 0.7829 71 L 0.0364 0.0855 0.8781 72 G 0.0284 0.0426 0.9290 73 T 0.2075 0.0145 0.7780 74 E 0.6671 0.0036 0.3293 75 V 0.8786 0.0041 0.1173 76 W 0.9251 0.0032 0.0717 77 V 0.9237 0.0035 0.0728 78 Q 0.9291 0.0032 0.0677 79 T 0.9235 0.0036 0.0729 80 Q 0.9225 0.0037 0.0737 81 I 0.9192 0.0033 0.0775 82 L 0.8603 0.0171 0.1226 83 G 0.7888 0.0130 0.1982 84 F 0.3719 0.0723 0.5558 85 D 0.1070 0.0622 0.8308 86 R 0.1791 0.0642 0.7568 87 K 0.6595 0.0285 0.3121 88 R 0.8873 0.0080 0.1048 89 L 0.9137 0.0044 0.0819 90 H 0.9193 0.0041 0.0766 91 V 0.9202 0.0042 0.0756 92 Y 0.9237 0.0037 0.0726 93 H 0.9189 0.0046 0.0764 94 S 0.9225 0.0045 0.0730 95 L 0.9180 0.0066 0.0754 96 H 0.8906 0.0105 0.0989 97 R 0.7963 0.0057 0.1980 98 A 0.1545 0.0853 0.7603 99 G 0.0358 0.0986 0.8657 100 F 0.0599 0.0290 0.9111 101 D 0.0924 0.0361 0.8715 102 E 0.6988 0.0157 0.2854 103 V 0.8861 0.0092 0.1047 104 L 0.8522 0.0284 0.1194 105 A 0.8540 0.0422 0.1038 106 A 0.8673 0.0315 0.1013 107 S 0.8779 0.0205 0.1016 108 E 0.8961 0.0136 0.0903 109 Q 0.9057 0.0097 0.0846 110 M 0.8998 0.0118 0.0885 111 L 0.9043 0.0127 0.0830 112 L 0.8989 0.0166 0.0844 113 H 0.8760 0.0206 0.1034 114 V 0.7848 0.0247 0.1905 115 D 0.4848 0.0182 0.4970 116 L 0.0266 0.1756 0.7978 117 A 0.0214 0.1453 0.8334 118 G 0.0749 0.1013 0.8239 119 P 0.1142 0.0428 0.8430 120 Q 0.3229 0.0250 0.6522 121 S 0.4180 0.0260 0.5560 122 A 0.2883 0.0416 0.6701 123 P 0.1809 0.0325 0.7866 124 F 0.0736 0.0228 0.9036 125 G 0.0544 0.0472 0.8984 126 H 0.0060 0.8830 0.1109 127 T 0.0051 0.9221 0.0728 128 T 0.0050 0.9354 0.0596 129 V 0.0049 0.9450 0.0501 130 C 0.0050 0.9307 0.0643 131 R 0.0052 0.9230 0.0718 132 L 0.0054 0.9243 0.0703 133 N 0.0052 0.9103 0.0845 134 H 0.0056 0.8762 0.1182 135 L 0.0079 0.8510 0.1411 136 V 0.0086 0.8421 0.1493 137 E 0.0086 0.7786 0.2128 138 Q 0.0155 0.6903 0.2942 139 Q 0.0307 0.5154 0.4538 140 E 0.0242 0.4331 0.5428 141 G 0.0320 0.3938 0.5742 142 A 0.0580 0.1625 0.7794 143 Q 0.0635 0.0989 0.8377 144 A 0.0934 0.0735 0.8331 145 P 0.0722 0.1191 0.8087 146 Q 0.0416 0.3744 0.5840 147 Y 0.0563 0.3971 0.5467 148 M 0.0882 0.3494 0.5624 149 G 0.1171 0.2555 0.6274 150 R 0.1973 0.2351 0.5676 151 T 0.3607 0.1996 0.4397 152 I 0.3498 0.1553 0.4949 153 K 0.2999 0.0775 0.6226 154 L 0.2200 0.0370 0.7430 155 P 0.1219 0.0206 0.8575 156 A 0.0490 0.0286 0.9224