# This file is the result of combining several RDB files, specifically # T0166.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0166.t2k.stride-ebghtl.rdb (weight 1.24869) # T0166.t2k.str.rdb (weight 1.53983) # T0166.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 T0166.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0166 # 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 T0166.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 341 # # ============================================ # Comments from T0166.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0166 # 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 T0166.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 341 # # ============================================ # Comments from T0166.t2k.str.rdb # ============================================ # TARGET T0166 # 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 T0166.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 341 # # ============================================ # Comments from T0166.t2k.alpha.rdb # ============================================ # TARGET T0166 # 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 T0166.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 341 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.0291 0.1860 0.7850 2 T 0.0243 0.5523 0.4234 3 D 0.0249 0.6823 0.2927 4 I 0.0058 0.9065 0.0876 5 L 0.0044 0.9424 0.0532 6 R 0.0044 0.9539 0.0416 7 E 0.0044 0.9569 0.0388 8 I 0.0044 0.9586 0.0370 9 G 0.0044 0.9567 0.0389 10 M 0.0044 0.9567 0.0388 11 I 0.0044 0.9544 0.0411 12 A 0.0045 0.9531 0.0424 13 R 0.0046 0.9453 0.0500 14 A 0.0047 0.9420 0.0533 15 L 0.0049 0.9336 0.0615 16 D 0.0056 0.9178 0.0766 17 S 0.0068 0.8996 0.0937 18 I 0.0081 0.8879 0.1040 19 S 0.0090 0.8685 0.1225 20 N 0.0079 0.8692 0.1229 21 I 0.0062 0.8770 0.1167 22 E 0.0059 0.8788 0.1153 23 F 0.0106 0.8407 0.1487 24 K 0.0127 0.7746 0.2127 25 E 0.0116 0.6769 0.3116 26 L 0.0480 0.2917 0.6604 27 S 0.0434 0.0439 0.9128 28 L 0.0762 0.0167 0.9071 29 T 0.0619 0.0216 0.9164 30 R 0.0098 0.8367 0.1535 31 G 0.0064 0.9031 0.0905 32 Q 0.0083 0.9362 0.0555 33 Y 0.0133 0.9436 0.0431 34 L 0.0238 0.9359 0.0404 35 Y 0.0269 0.9352 0.0378 36 L 0.0276 0.9329 0.0395 37 V 0.0188 0.9405 0.0407 38 R 0.0174 0.9339 0.0487 39 V 0.0223 0.8937 0.0840 40 C 0.0247 0.8046 0.1707 41 E 0.0357 0.5998 0.3645 42 N 0.0693 0.1991 0.7316 43 P 0.0390 0.1007 0.8603 44 G 0.0529 0.0593 0.8878 45 I 0.1462 0.0258 0.8281 46 I 0.1454 0.0247 0.8299 47 Q 0.0078 0.9073 0.0849 48 E 0.0045 0.9339 0.0617 49 K 0.0048 0.9438 0.0515 50 I 0.0047 0.9503 0.0451 51 A 0.0048 0.9456 0.0496 52 E 0.0051 0.9315 0.0634 53 L 0.0061 0.8799 0.1140 54 I 0.0431 0.5556 0.4013 55 K 0.0329 0.0945 0.8726 56 V 0.0731 0.0440 0.8829 57 D 0.0682 0.0326 0.8991 58 R 0.0242 0.7091 0.2667 59 T 0.0085 0.8538 0.1377 60 T 0.0104 0.8846 0.1050 61 A 0.0050 0.9362 0.0587 62 A 0.0045 0.9502 0.0453 63 R 0.0044 0.9553 0.0403 64 A 0.0044 0.9563 0.0393 65 I 0.0044 0.9579 0.0377 66 K 0.0045 0.9570 0.0385 67 R 0.0045 0.9560 0.0395 68 L 0.0045 0.9521 0.0434 69 E 0.0049 0.9332 0.0619 70 E 0.0062 0.8428 0.1510 71 Q 0.0437 0.2681 0.6882 72 G 0.0330 0.0260 0.9410 73 F 0.1655 0.0284 0.8062 74 I 0.7291 0.0142 0.2568 75 Y 0.7967 0.0236 0.1797 76 R 0.7855 0.0164 0.1981 77 Q 0.6407 0.0111 0.3482 78 E 0.3958 0.0122 0.5920 79 D 0.1367 0.0132 0.8501 80 A 0.0152 0.3154 0.6694 81 S 0.0190 0.2481 0.7329 82 N 0.0817 0.2534 0.6648 83 K 0.1109 0.1250 0.7641 84 K 0.4786 0.0613 0.4602 85 I 0.7794 0.0184 0.2022 86 K 0.8188 0.0140 0.1672 87 R 0.8687 0.0087 0.1226 88 I 0.8645 0.0077 0.1278 89 Y 0.7961 0.0099 0.1940 90 A 0.5194 0.0135 0.4671 91 T 0.1011 0.0222 0.8767 92 E 0.0081 0.7999 0.1920 93 K 0.0109 0.8588 0.1304 94 G 0.0073 0.9048 0.0879 95 K 0.0050 0.9441 0.0509 96 N 0.0049 0.9428 0.0523 97 V 0.0051 0.9405 0.0544 98 Y 0.0053 0.9329 0.0618 99 P 0.0058 0.9251 0.0692 100 I 0.0066 0.9038 0.0896 101 I 0.0084 0.8800 0.1117 102 V 0.0075 0.8918 0.1007 103 R 0.0053 0.9075 0.0872 104 E 0.0055 0.9161 0.0784 105 N 0.0053 0.9280 0.0667 106 Q 0.0048 0.9414 0.0538 107 H 0.0048 0.9477 0.0475 108 S 0.0046 0.9465 0.0489 109 N 0.0045 0.9469 0.0486 110 Q 0.0047 0.9429 0.0525 111 V 0.0050 0.9314 0.0636 112 A 0.0053 0.9045 0.0902 113 L 0.0070 0.8468 0.1462 114 Q 0.0121 0.5841 0.4037 115 G 0.0175 0.3006 0.6819 116 L 0.0553 0.0749 0.8698 117 S 0.0461 0.0302 0.9237 118 E 0.0047 0.9149 0.0803 119 V 0.0045 0.9393 0.0562 120 E 0.0045 0.9503 0.0452 121 I 0.0044 0.9592 0.0364 122 S 0.0044 0.9576 0.0380 123 Q 0.0044 0.9549 0.0407 124 L 0.0044 0.9567 0.0389 125 A 0.0044 0.9592 0.0364 126 D 0.0044 0.9588 0.0368 127 Y 0.0044 0.9582 0.0374 128 L 0.0044 0.9591 0.0365 129 V 0.0044 0.9585 0.0371 130 R 0.0044 0.9542 0.0414 131 M 0.0045 0.9483 0.0472 132 R 0.0049 0.9305 0.0646 133 K 0.0075 0.8243 0.1682 134 N 0.0164 0.6195 0.3641 135 V 0.0317 0.4787 0.4896 136 S 0.0281 0.4657 0.5062 137 E 0.0318 0.4071 0.5611 138 D 0.0292 0.4758 0.4949 139 W 0.0535 0.5834 0.3631 140 E 0.0815 0.6164 0.3021 141 F 0.1291 0.5722 0.2987 142 V 0.1201 0.4847 0.3953 143 K 0.1047 0.3920 0.5033 144 K 0.0385 0.2157 0.7458 145 G 0.0420 0.0812 0.8768 146 N 0.1167 0.0521 0.8312 147 T 0.1610 0.1069 0.7321 148 R 0.1497 0.1114 0.7389 149 N 0.1222 0.0796 0.7981 150 Y 0.0371 0.0430 0.9199