# This file is the result of combining several RDB files, specifically # T0317.t06.dssp-ebghstl.rdb (weight 1.53986) # T0317.t06.stride-ebghtl.rdb (weight 1.24869) # T0317.t06.str2.rdb (weight 1.54758) # T0317.t06.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 T0317.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0317 # 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 T0317.t06-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 1764 # # ============================================ # Comments from T0317.t06.stride-ebghtl.rdb # ============================================ # TARGET T0317 # Using neural net t06-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 T0317.t06-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 1764 # # ============================================ # Comments from T0317.t06.str2.rdb # ============================================ # TARGET T0317 # 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 T0317.t06-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 1764 # # ============================================ # Comments from T0317.t06.alpha.rdb # ============================================ # TARGET T0317 # Using neural net t06-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 T0317.t06-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 1764 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0527 0.0520 0.8952 2 G 0.0765 0.0395 0.8839 3 T 0.1190 0.0779 0.8031 4 S 0.1580 0.1720 0.6700 5 E 0.2094 0.1934 0.5971 6 A 0.1920 0.1046 0.7035 7 A 0.1190 0.0472 0.8339 8 P 0.0839 0.0285 0.8876 9 P 0.0759 0.0354 0.8887 10 P 0.1054 0.0727 0.8220 11 F 0.1042 0.3004 0.5954 12 A 0.1467 0.3826 0.4707 13 R 0.2971 0.3295 0.3735 14 V 0.4183 0.1566 0.4251 15 A 0.2338 0.0669 0.6993 16 P 0.0871 0.1970 0.7160 17 A 0.1604 0.1669 0.6727 18 L 0.5413 0.0928 0.3659 19 F 0.7050 0.0533 0.2417 20 I 0.6223 0.0807 0.2970 21 G 0.2747 0.0641 0.6613 22 N 0.1585 0.0908 0.7506 23 A 0.1473 0.2744 0.5784 24 R 0.1317 0.3907 0.4776 25 A 0.1031 0.4458 0.4511 26 A 0.0567 0.5384 0.4049 27 G 0.0456 0.4325 0.5219 28 A 0.0588 0.5070 0.4342 29 T 0.0104 0.8567 0.1329 30 E 0.0051 0.9369 0.0580 31 L 0.0047 0.9533 0.0420 32 L 0.0050 0.9562 0.0388 33 V 0.0052 0.9488 0.0460 34 R 0.0059 0.9182 0.0759 35 A 0.0426 0.3879 0.5695 36 G 0.0479 0.0127 0.9394 37 I 0.1381 0.0059 0.8560 38 T 0.4461 0.0309 0.5230 39 L 0.9240 0.0033 0.0727 40 C 0.9322 0.0032 0.0646 41 V 0.9320 0.0033 0.0647 42 N 0.9091 0.0035 0.0875 43 V 0.6821 0.0091 0.3088 44 S 0.4220 0.0204 0.5576 45 R 0.2216 0.0473 0.7311 46 Q 0.1491 0.0471 0.8038 47 Q 0.1063 0.0273 0.8664 48 P 0.0662 0.0580 0.8759 49 G 0.0737 0.0326 0.8936 50 P 0.0769 0.0600 0.8631 51 R 0.0961 0.0481 0.8558 52 A 0.1037 0.0426 0.8538 53 P 0.1020 0.0914 0.8066 54 G 0.3089 0.0678 0.6234 55 V 0.6590 0.0211 0.3200 56 A 0.7701 0.0213 0.2085 57 E 0.8914 0.0080 0.1006 58 L 0.8865 0.0070 0.1064 59 R 0.8505 0.0073 0.1422 60 V 0.6402 0.0079 0.3519 61 P 0.3850 0.0137 0.6013 62 V 0.1988 0.0402 0.7610 63 F 0.1116 0.0698 0.8186 64 D 0.0829 0.0756 0.8415 65 D 0.0605 0.0735 0.8660 66 P 0.0468 0.1556 0.7976 67 A 0.0620 0.2950 0.6430 68 E 0.0344 0.5065 0.4591 69 D 0.0519 0.5163 0.4318 70 L 0.0253 0.6894 0.2853 71 L 0.0178 0.7590 0.2232 72 T 0.0121 0.7535 0.2343 73 H 0.0135 0.7405 0.2460 74 L 0.0074 0.8728 0.1197 75 E 0.0049 0.9434 0.0517 76 P 0.0048 0.9512 0.0441 77 T 0.0047 0.9580 0.0373 78 C 0.0047 0.9586 0.0367 79 A 0.0047 0.9598 0.0356 80 A 0.0047 0.9580 0.0373 81 M 0.0047 0.9563 0.0390 82 E 0.0047 0.9537 0.0416 83 A 0.0050 0.9388 0.0562 84 A 0.0062 0.9249 0.0689 85 V 0.0148 0.8717 0.1135 86 R 0.0153 0.7553 0.2293 87 D 0.0388 0.2572 0.7040 88 G 0.0328 0.0253 0.9419 89 G 0.0667 0.0135 0.9199 90 S 0.4510 0.0063 0.5427 91 C 0.9041 0.0037 0.0922 92 L 0.9308 0.0033 0.0660 93 V 0.9295 0.0032 0.0673 94 Y 0.8930 0.0042 0.1028 95 C 0.5368 0.0151 0.4481 96 K 0.1494 0.0980 0.7527 97 N 0.0983 0.0877 0.8140 98 G 0.0724 0.0948 0.8328 99 R 0.1211 0.1540 0.7248 100 S 0.1375 0.2284 0.6341 101 R 0.0394 0.6605 0.3002 102 S 0.0202 0.8554 0.1244 103 A 0.0058 0.9488 0.0454 104 A 0.0047 0.9594 0.0359 105 V 0.0047 0.9602 0.0351 106 C 0.0047 0.9605 0.0348 107 T 0.0047 0.9609 0.0345 108 A 0.0046 0.9610 0.0343 109 Y 0.0047 0.9601 0.0352 110 L 0.0047 0.9592 0.0361 111 M 0.0048 0.9555 0.0398 112 R 0.0051 0.9458 0.0491 113 H 0.0071 0.8945 0.0984 114 R 0.0440 0.3031 0.6529 115 G 0.0411 0.0164 0.9425 116 H 0.0735 0.0093 0.9172 117 S 0.1138 0.0083 0.8778 118 L 0.0049 0.9453 0.0499 119 D 0.0047 0.9605 0.0349 120 R 0.0047 0.9605 0.0348 121 A 0.0046 0.9613 0.0341 122 F 0.0047 0.9607 0.0346 123 Q 0.0046 0.9608 0.0346 124 M 0.0047 0.9596 0.0357 125 V 0.0048 0.9537 0.0415 126 K 0.0054 0.9376 0.0570 127 S 0.0079 0.8372 0.1549 128 A 0.0226 0.6000 0.3773 129 R 0.0659 0.1084 0.8257 130 P 0.0341 0.1950 0.7709 131 V 0.0778 0.1970 0.7252 132 A 0.2039 0.1308 0.6653 133 E 0.2166 0.0505 0.7329 134 P 0.1421 0.0475 0.8104 135 N 0.0679 0.0473 0.8848 136 L 0.0055 0.9042 0.0904 137 G 0.0055 0.9187 0.0758 138 F 0.0048 0.9502 0.0450 139 W 0.0047 0.9600 0.0354 140 A 0.0047 0.9608 0.0346 141 Q 0.0047 0.9600 0.0354 142 L 0.0047 0.9603 0.0351 143 Q 0.0047 0.9597 0.0356 144 K 0.0047 0.9566 0.0387 145 Y 0.0048 0.9513 0.0439 146 E 0.0048 0.9535 0.0418 147 Q 0.0047 0.9516 0.0436 148 T 0.0049 0.9434 0.0517 149 L 0.0053 0.9225 0.0722 150 Q 0.0075 0.8479 0.1446 151 A 0.0139 0.6779 0.3083 152 Q 0.0350 0.4845 0.4805 153 A 0.0698 0.2871 0.6432 154 I 0.1303 0.1452 0.7245 155 L 0.1061 0.0590 0.8349 156 P 0.0852 0.0605 0.8543 157 R 0.0822 0.0743 0.8435 158 E 0.0940 0.0400 0.8660 159 P 0.0996 0.0575 0.8429 160 I 0.1111 0.0492 0.8397 161 D 0.1013 0.0195 0.8792 162 P 0.0404 0.0837 0.8759 163 E 0.0341 0.0485 0.9174