# This file is the result of combining several RDB files, specifically # T0327.t04.dssp-ebghstl.rdb (weight 1.53986) # T0327.t04.stride-ebghtl.rdb (weight 1.24869) # T0327.t04.str2.rdb (weight 1.54758) # T0327.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 T0327.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # Using neural net t04-2621-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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.str2.rdb # ============================================ # TARGET T0327 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.53018 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0755 0.2012 0.7233 2 N 0.0700 0.1865 0.7436 3 K 0.0341 0.3450 0.6209 4 D 0.0412 0.3155 0.6433 5 K 0.0516 0.6990 0.2494 6 L 0.0994 0.7157 0.1849 7 R 0.0660 0.8459 0.0881 8 Y 0.0619 0.8788 0.0593 9 A 0.0393 0.9120 0.0487 10 I 0.0415 0.9111 0.0474 11 L 0.0299 0.9139 0.0562 12 K 0.0158 0.9303 0.0539 13 E 0.0137 0.9278 0.0585 14 I 0.0189 0.8603 0.1209 15 F 0.0558 0.5869 0.3573 16 E 0.0805 0.1939 0.7256 17 G 0.0494 0.0473 0.9033 18 N 0.0836 0.0401 0.8763 19 T 0.1200 0.0189 0.8610 20 P 0.1169 0.0367 0.8464 21 L 0.1589 0.0307 0.8104 22 S 0.1113 0.0229 0.8658 23 E 0.0184 0.5387 0.4428 24 N 0.0209 0.4522 0.5270 25 D 0.0538 0.5077 0.4385 26 I 0.2777 0.1426 0.5797 27 G 0.3280 0.0684 0.6036 28 V 0.3245 0.0292 0.6462 29 T 0.1148 0.0254 0.8598 30 E 0.0066 0.8816 0.1117 31 D 0.0050 0.9042 0.0907 32 Q 0.0054 0.9300 0.0646 33 F 0.0051 0.9510 0.0439 34 D 0.0047 0.9557 0.0396 35 D 0.0047 0.9545 0.0407 36 A 0.0047 0.9570 0.0383 37 V 0.0047 0.9593 0.0361 38 N 0.0047 0.9565 0.0388 39 F 0.0047 0.9464 0.0489 40 L 0.0070 0.9348 0.0582 41 K 0.0077 0.8651 0.1272 42 R 0.0108 0.6558 0.3334 43 E 0.0443 0.2045 0.7513 44 G 0.0351 0.0278 0.9371 45 Y 0.2496 0.0148 0.7356 46 I 0.7969 0.0061 0.1970 47 I 0.7814 0.0290 0.1896 48 G 0.8217 0.0110 0.1673 49 V 0.8426 0.0059 0.1516 50 H 0.8649 0.0042 0.1309 51 Y 0.7310 0.0094 0.2595 52 S 0.2475 0.0228 0.7297 53 D 0.0345 0.0998 0.8657 54 D 0.0315 0.0655 0.9030 55 R 0.0900 0.0391 0.8709 56 P 0.1289 0.0888 0.7823 57 H 0.3920 0.1505 0.4575 58 L 0.5915 0.1561 0.2525 59 Y 0.5778 0.1486 0.2736 60 K 0.5377 0.0965 0.3658 61 L 0.3036 0.0857 0.6107 62 G 0.1184 0.0471 0.8344 63 P 0.0532 0.2532 0.6936 64 E 0.0846 0.2834 0.6320 65 L 0.1884 0.2177 0.5939 66 T 0.1312 0.1447 0.7241 67 E 0.0595 0.5152 0.4253 68 K 0.0437 0.4685 0.4878 69 G 0.0274 0.5996 0.3730 70 E 0.0232 0.8270 0.1498 71 N 0.0151 0.8643 0.1206 72 Y 0.0094 0.8729 0.1177 73 L 0.0258 0.7958 0.1784 74 K 0.0161 0.7248 0.2591 75 E 0.0163 0.5251 0.4586 76 N 0.0538 0.2945 0.6517 77 G 0.0305 0.4627 0.5068 78 T 0.0343 0.5530 0.4127 79 W 0.0191 0.8174 0.1636 80 S 0.0116 0.8799 0.1086 81 K 0.0058 0.9431 0.0511 82 A 0.0052 0.9533 0.0415 83 Y 0.0058 0.9498 0.0444 84 K 0.0057 0.9468 0.0475 85 T 0.0065 0.9435 0.0500 86 I 0.0069 0.9404 0.0527 87 K 0.0070 0.9456 0.0475 88 E 0.0062 0.9423 0.0515 89 I 0.0088 0.9174 0.0738 90 K 0.0079 0.9062 0.0859 91 D 0.0144 0.8326 0.1531 92 W 0.0312 0.7471 0.2217 93 I 0.1157 0.4066 0.4777 94 K 0.1353 0.3094 0.5553 95 L 0.0712 0.5033 0.4254 96 E 0.1039 0.4722 0.4239 97 H 0.1134 0.4313 0.4553 98 H 0.1039 0.3181 0.5780 99 H 0.1054 0.2192 0.6753 100 H 0.1141 0.1724 0.7135 101 H 0.1099 0.1142 0.7760 102 H 0.0621 0.0568 0.8811