# This file is the result of combining several RDB files, specifically # T0265.t04.dssp-ebghstl.rdb (weight 1.53986) # T0265.t04.stride-ebghtl.rdb (weight 1.24869) # T0265.t04.str2.rdb (weight 1.54758) # T0265.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 T0265.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0265 # 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 T0265.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 46.7518 # # ============================================ # Comments from T0265.t04.stride-ebghtl.rdb # ============================================ # TARGET T0265 # 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 T0265.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 46.7518 # # ============================================ # Comments from T0265.t04.str2.rdb # ============================================ # TARGET T0265 # Using neural net t04-2621-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 T0265.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 46.7518 # # ============================================ # Comments from T0265.t04.alpha.rdb # ============================================ # TARGET T0265 # 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 T0265.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 46.7518 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0898 0.2590 0.6511 2 M 0.1071 0.4751 0.4178 3 K 0.0997 0.6323 0.2680 4 E 0.0930 0.6263 0.2807 5 K 0.0795 0.6047 0.3158 6 L 0.0651 0.4279 0.5070 7 E 0.0261 0.5230 0.4509 8 S 0.0195 0.5553 0.4252 9 K 0.0218 0.5899 0.3883 10 K 0.0417 0.5937 0.3647 11 D 0.0366 0.6811 0.2823 12 E 0.0416 0.8366 0.1218 13 I 0.0644 0.8405 0.0952 14 R 0.0715 0.8257 0.1027 15 C 0.0797 0.7884 0.1319 16 C 0.0943 0.6999 0.2058 17 Y 0.1445 0.4262 0.4294 18 K 0.0933 0.1131 0.7935 19 I 0.0990 0.0283 0.8727 20 T 0.0549 0.0458 0.8993 21 D 0.0059 0.9010 0.0931 22 T 0.0056 0.9424 0.0520 23 D 0.0056 0.9522 0.0421 24 V 0.0047 0.9585 0.0367 25 A 0.0047 0.9608 0.0345 26 V 0.0053 0.9602 0.0345 27 L 0.0056 0.9591 0.0353 28 L 0.0053 0.9601 0.0346 29 K 0.0048 0.9573 0.0379 30 M 0.0052 0.9425 0.0523 31 V 0.0081 0.9002 0.0917 32 E 0.0167 0.7528 0.2305 33 I 0.0460 0.4585 0.4955 34 E 0.0441 0.1709 0.7850 35 K 0.0628 0.0275 0.9096 36 P 0.1002 0.0284 0.8714 37 I 0.1795 0.0107 0.8098 38 T 0.1122 0.0112 0.8765 39 S 0.0048 0.9499 0.0453 40 E 0.0047 0.9601 0.0353 41 E 0.0047 0.9602 0.0351 42 L 0.0047 0.9598 0.0355 43 A 0.0048 0.9546 0.0406 44 D 0.0056 0.9320 0.0624 45 I 0.0079 0.8800 0.1122 46 F 0.0567 0.5439 0.3994 47 K 0.0475 0.1455 0.8070 48 L 0.0696 0.1016 0.8288 49 S 0.0488 0.1474 0.8038 50 K 0.0224 0.7011 0.2765 51 T 0.0386 0.7502 0.2113 52 T 0.0448 0.8021 0.1531 53 V 0.0057 0.9506 0.0437 54 E 0.0050 0.9562 0.0389 55 N 0.0047 0.9594 0.0360 56 S 0.0047 0.9551 0.0402 57 L 0.0047 0.9591 0.0362 58 K 0.0047 0.9609 0.0345 59 K 0.0047 0.9607 0.0346 60 L 0.0047 0.9583 0.0370 61 I 0.0048 0.9467 0.0485 62 E 0.0053 0.8736 0.1211 63 L 0.0422 0.2922 0.6657 64 G 0.0385 0.0230 0.9385 65 L 0.2051 0.0215 0.7734 66 V 0.7681 0.0076 0.2243 67 V 0.8652 0.0067 0.1281 68 R 0.8932 0.0053 0.1015 69 T 0.8492 0.0105 0.1403 70 K 0.8230 0.0120 0.1650 71 T 0.6667 0.0241 0.3093 72 E 0.4499 0.0471 0.5030 73 G 0.2971 0.0634 0.6395 74 K 0.2944 0.0871 0.6184 75 K 0.3144 0.1076 0.5780 76 I 0.2224 0.0715 0.7061 77 G 0.2155 0.0296 0.7549 78 R 0.2927 0.0123 0.6950 79 P 0.4677 0.0106 0.5217 80 K 0.6495 0.0243 0.3262 81 Y 0.8613 0.0063 0.1324 82 Y 0.9064 0.0046 0.0889 83 Y 0.8992 0.0070 0.0939 84 S 0.8060 0.0089 0.1850 85 I 0.4187 0.0239 0.5575 86 S 0.0966 0.0292 0.8742 87 S 0.0116 0.7276 0.2608 88 N 0.0092 0.8764 0.1145 89 I 0.0058 0.9345 0.0597 90 L 0.0048 0.9546 0.0407 91 E 0.0047 0.9593 0.0360 92 K 0.0047 0.9583 0.0369 93 I 0.0047 0.9557 0.0396 94 R 0.0047 0.9577 0.0376 95 N 0.0050 0.9540 0.0411 96 D 0.0050 0.9450 0.0500 97 L 0.0047 0.9562 0.0391 98 L 0.0048 0.9554 0.0398 99 N 0.0049 0.9507 0.0444 100 C 0.0053 0.9406 0.0541 101 A 0.0058 0.9384 0.0557 102 K 0.0062 0.9276 0.0661 103 R 0.0079 0.9043 0.0878 104 M 0.0238 0.8245 0.1516 105 E 0.0403 0.6197 0.3401 106 L 0.0571 0.4656 0.4773 107 A 0.0574 0.2066 0.7360 108 A 0.0644 0.0971 0.8386 109 T 0.0613 0.0746 0.8641