# This file is the result of combining several RDB files, specifically # T0408.t04.dssp-ebghstl.rdb (weight 1.53986) # T0408.t04.stride-ebghtl.rdb (weight 1.24869) # T0408.t04.str2.rdb (weight 1.54758) # T0408.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 T0408.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 904 # # ============================================ # Comments from T0408.t04.stride-ebghtl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 904 # # ============================================ # Comments from T0408.t04.str2.rdb # ============================================ # TARGET T0408 # 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 T0408.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 904 # # ============================================ # Comments from T0408.t04.alpha.rdb # ============================================ # TARGET T0408 # 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 T0408.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 904 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0769 0.0645 0.8586 2 K 0.0535 0.1609 0.7856 3 N 0.0502 0.3277 0.6221 4 E 0.0506 0.4447 0.5047 5 V 0.0776 0.4905 0.4319 6 F 0.1092 0.4304 0.4604 7 F 0.0767 0.4501 0.4732 8 G 0.0310 0.7068 0.2622 9 E 0.0125 0.8056 0.1818 10 G 0.0126 0.8610 0.1264 11 M 0.0086 0.9207 0.0707 12 K 0.0065 0.9324 0.0611 13 V 0.0067 0.9298 0.0635 14 V 0.0073 0.9097 0.0830 15 K 0.0085 0.8631 0.1284 16 E 0.0075 0.8010 0.1915 17 K 0.0159 0.6465 0.3376 18 Y 0.0797 0.1674 0.7529 19 P 0.0082 0.8335 0.1582 20 D 0.0066 0.8980 0.0954 21 L 0.0053 0.9449 0.0498 22 Y 0.0048 0.9579 0.0374 23 D 0.0047 0.9602 0.0351 24 I 0.0050 0.9589 0.0361 25 I 0.0047 0.9547 0.0406 26 V 0.0049 0.9425 0.0526 27 K 0.0055 0.9148 0.0797 28 L 0.0093 0.8571 0.1336 29 N 0.0187 0.7796 0.2017 30 D 0.0133 0.7465 0.2402 31 T 0.0326 0.7367 0.2307 32 V 0.0798 0.6434 0.2768 33 F 0.1028 0.5127 0.3845 34 T 0.0812 0.3338 0.5850 35 G 0.0546 0.1353 0.8100 36 K 0.0345 0.1467 0.8188 37 T 0.0852 0.1375 0.7773 38 L 0.1183 0.0557 0.8260 39 D 0.0912 0.0668 0.8420 40 Y 0.0162 0.8428 0.1410 41 K 0.0090 0.9280 0.0630 42 T 0.0089 0.9378 0.0533 43 Q 0.0051 0.9566 0.0383 44 K 0.0049 0.9589 0.0362 45 L 0.0051 0.9584 0.0365 46 I 0.0048 0.9596 0.0356 47 A 0.0047 0.9609 0.0344 48 I 0.0047 0.9605 0.0348 49 G 0.0050 0.9585 0.0365 50 I 0.0051 0.9516 0.0433 51 V 0.0070 0.9230 0.0700 52 A 0.0189 0.8176 0.1635 53 S 0.0428 0.5283 0.4289 54 R 0.0434 0.1672 0.7894 55 C 0.0585 0.0854 0.8561 56 D 0.0324 0.1948 0.7729 57 E 0.0184 0.6236 0.3579 58 V 0.0070 0.8857 0.1073 59 A 0.0063 0.9245 0.0692 60 I 0.0049 0.9476 0.0475 61 E 0.0052 0.9533 0.0415 62 K 0.0052 0.9528 0.0420 63 Q 0.0047 0.9516 0.0437 64 M 0.0047 0.9592 0.0362 65 K 0.0046 0.9616 0.0338 66 S 0.0047 0.9606 0.0348 67 A 0.0047 0.9606 0.0347 68 M 0.0047 0.9580 0.0373 69 K 0.0049 0.9305 0.0646 70 E 0.0058 0.8041 0.1901 71 L 0.0458 0.4128 0.5414 72 G 0.0487 0.0215 0.9297 73 I 0.0747 0.0086 0.9167 74 T 0.0585 0.0109 0.9306 75 K 0.0048 0.9512 0.0439 76 E 0.0047 0.9606 0.0347 77 E 0.0047 0.9610 0.0343 78 I 0.0046 0.9614 0.0340 79 A 0.0046 0.9615 0.0338 80 D 0.0046 0.9614 0.0340 81 V 0.0047 0.9610 0.0344 82 L 0.0047 0.9603 0.0351 83 R 0.0046 0.9615 0.0339 84 V 0.0046 0.9603 0.0350 85 V 0.0047 0.9587 0.0366 86 L 0.0047 0.9549 0.0404 87 L 0.0054 0.9431 0.0515 88 T 0.0090 0.8751 0.1159 89 S 0.0230 0.6624 0.3146 90 G 0.0200 0.4566 0.5235 91 M 0.0176 0.7187 0.2637 92 P 0.0069 0.9039 0.0892 93 A 0.0054 0.9241 0.0704 94 F 0.0050 0.9476 0.0474 95 T 0.0048 0.9505 0.0447 96 K 0.0048 0.9466 0.0486 97 A 0.0049 0.9545 0.0406 98 M 0.0047 0.9582 0.0371 99 K 0.0047 0.9582 0.0370 100 I 0.0049 0.9490 0.0460 101 L 0.0050 0.9304 0.0646 102 E 0.0052 0.8376 0.1572 103 K 0.0074 0.6949 0.2977 104 L 0.0237 0.2323 0.7440