# This file is the result of combining several RDB files, specifically # T0639.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0639.t2k.stride-ebghtl.rdb (weight 1.24869) # T0639.t2k.str.rdb (weight 1.53983) # 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 T0639.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.str.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0133 0.1060 0.8807 2 N 0.0337 0.3651 0.6012 3 A 0.0212 0.5480 0.4308 4 M 0.0169 0.6451 0.3380 5 E 0.0209 0.6442 0.3349 6 T 0.0217 0.6658 0.3125 7 L 0.0089 0.8650 0.1260 8 N 0.0063 0.9204 0.0734 9 D 0.0055 0.9442 0.0504 10 I 0.0038 0.9641 0.0322 11 K 0.0037 0.9697 0.0266 12 K 0.0037 0.9700 0.0262 13 I 0.0040 0.9682 0.0277 14 L 0.0043 0.9634 0.0322 15 I 0.0044 0.9526 0.0430 16 N 0.0056 0.9047 0.0897 17 V 0.0099 0.7304 0.2597 18 G 0.0389 0.2521 0.7090 19 L 0.1148 0.2590 0.6262 20 Y 0.1595 0.2950 0.5455 21 Q 0.1238 0.2211 0.6551 22 G 0.1528 0.0822 0.7650 23 F 0.3183 0.0479 0.6338 24 D 0.3315 0.0436 0.6249 25 L 0.2086 0.1492 0.6422 26 T 0.1648 0.1219 0.7133 27 D 0.1163 0.1209 0.7628 28 P 0.0819 0.2099 0.7082 29 K 0.1341 0.2211 0.6448 30 V 0.2184 0.2367 0.5449 31 S 0.2189 0.2277 0.5533 32 E 0.2321 0.3211 0.4467 33 E 0.2184 0.3148 0.4668 34 V 0.1524 0.2559 0.5916 35 N 0.0961 0.1505 0.7534 36 H 0.0717 0.1590 0.7692 37 E 0.0826 0.1524 0.7650 38 T 0.1081 0.1334 0.7585 39 A 0.1489 0.1452 0.7059 40 N 0.1725 0.1335 0.6940 41 M 0.2708 0.4242 0.3050 42 K 0.3567 0.4445 0.1988 43 W 0.3691 0.4758 0.1551 44 I 0.2920 0.4918 0.2162 45 K 0.2470 0.4584 0.2945 46 D 0.1638 0.4062 0.4300 47 Y 0.2165 0.2075 0.5759 48 T 0.1328 0.1045 0.7628 49 S 0.0639 0.1085 0.8276 50 D 0.0265 0.0840 0.8896 51 G 0.0262 0.1214 0.8525 52 N 0.0531 0.1169 0.8300 53 W 0.0475 0.3287 0.6238 54 D 0.0224 0.4600 0.5176 55 N 0.0118 0.7287 0.2596 56 E 0.0114 0.8164 0.1722 57 F 0.0079 0.8617 0.1304 58 K 0.0076 0.8832 0.1092 59 E 0.0060 0.8902 0.1038 60 D 0.0061 0.8660 0.1279 61 L 0.0038 0.9430 0.0532 62 K 0.0038 0.9451 0.0511 63 N 0.0038 0.9292 0.0670 64 F 0.0038 0.9473 0.0490 65 L 0.0038 0.9533 0.0429 66 D 0.0038 0.9211 0.0751 67 Y 0.0038 0.9031 0.0930 68 M 0.0057 0.9034 0.0908 69 E 0.0081 0.9089 0.0830 70 V 0.0098 0.9153 0.0749 71 C 0.0181 0.9034 0.0785 72 Q 0.0423 0.8484 0.1094 73 L 0.0683 0.7927 0.1390 74 A 0.0806 0.6972 0.2222 75 L 0.1107 0.4664 0.4229 76 N 0.0675 0.2474 0.6852 77 D 0.0192 0.4063 0.5745 78 K 0.0144 0.5357 0.4499 79 N 0.0231 0.5627 0.4143 80 F 0.0347 0.7287 0.2366 81 K 0.0429 0.7765 0.1806 82 I 0.0430 0.7810 0.1760 83 A 0.0334 0.7722 0.1945 84 S 0.0230 0.7770 0.2001 85 N 0.0153 0.7807 0.2040 86 S 0.0226 0.7813 0.1960 87 L 0.0240 0.8694 0.1066 88 F 0.0240 0.9047 0.0713 89 M 0.0173 0.9265 0.0562 90 A 0.0194 0.9297 0.0509 91 M 0.0266 0.9235 0.0498 92 I 0.0361 0.9010 0.0629 93 Y 0.0331 0.8654 0.1014 94 A 0.0260 0.7841 0.1898 95 G 0.0300 0.5399 0.4301 96 N 0.0459 0.4501 0.5040 97 L 0.0094 0.9062 0.0844 98 S 0.0048 0.9447 0.0505 99 L 0.0055 0.9478 0.0467 100 I 0.0048 0.9544 0.0409 101 F 0.0044 0.9538 0.0418 102 D 0.0048 0.9389 0.0562 103 S 0.0056 0.9050 0.0893 104 I 0.0087 0.8984 0.0930 105 K 0.0083 0.8921 0.0996 106 T 0.0064 0.8739 0.1198 107 D 0.0088 0.8619 0.1294 108 I 0.0045 0.9411 0.0544 109 S 0.0048 0.9522 0.0429 110 T 0.0063 0.9430 0.0507 111 L 0.0136 0.9092 0.0772 112 L 0.0271 0.8266 0.1462 113 S 0.0387 0.7189 0.2424 114 A 0.0411 0.6275 0.3314 115 E 0.0685 0.5743 0.3572 116 Y 0.0845 0.4637 0.4518 117 K 0.0843 0.3527 0.5630 118 K 0.0675 0.2628 0.6697 119 N 0.0697 0.1562 0.7742 120 S 0.0871 0.1106 0.8023 121 F 0.1493 0.0975 0.7532 122 S 0.1451 0.0899 0.7650 123 W 0.1023 0.1078 0.7899 124 P 0.0690 0.1845 0.7464 125 S 0.0817 0.2147 0.7035 126 L 0.0904 0.1313 0.7782 127 D 0.0458 0.0592 0.8949 128 E 0.0105 0.0158 0.9737