# This file is the result of combining several RDB files, specifically # T0236.t04.dssp-ebghstl.rdb (weight 1.53986) # T0236.t04.stride-ebghtl.rdb (weight 1.24869) # T0236.t04.str2.rdb (weight 1.54758) # T0236.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 T0236.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0236 # 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 T0236.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 5.42082 # # ============================================ # Comments from T0236.t04.stride-ebghtl.rdb # ============================================ # TARGET T0236 # 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 T0236.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 5.42082 # # ============================================ # Comments from T0236.t04.str2.rdb # ============================================ # TARGET T0236 # 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 T0236.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 5.42082 # # ============================================ # Comments from T0236.t04.alpha.rdb # ============================================ # TARGET T0236 # 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 T0236.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 5.42082 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0717 0.2691 0.6592 2 D 0.0844 0.5190 0.3967 3 F 0.0217 0.8422 0.1361 4 R 0.0066 0.9308 0.0626 5 E 0.0060 0.9467 0.0473 6 V 0.0062 0.9471 0.0466 7 I 0.0057 0.9415 0.0529 8 E 0.0051 0.9485 0.0464 9 Q 0.0050 0.9488 0.0462 10 R 0.0048 0.9485 0.0467 11 Y 0.0047 0.9557 0.0396 12 H 0.0047 0.9601 0.0353 13 Q 0.0047 0.9600 0.0353 14 L 0.0047 0.9595 0.0359 15 L 0.0047 0.9582 0.0371 16 S 0.0047 0.9579 0.0374 17 R 0.0049 0.9501 0.0450 18 Y 0.0053 0.9404 0.0544 19 I 0.0062 0.9152 0.0786 20 A 0.0099 0.8529 0.1372 21 E 0.0226 0.7049 0.2725 22 L 0.0457 0.4743 0.4800 23 T 0.0482 0.2682 0.6836 24 E 0.0077 0.9036 0.0887 25 T 0.0087 0.9278 0.0635 26 S 0.0081 0.9294 0.0624 27 L 0.0082 0.9392 0.0526 28 Y 0.0076 0.9400 0.0524 29 Q 0.0096 0.9325 0.0579 30 A 0.0103 0.9269 0.0628 31 Q 0.0116 0.9168 0.0715 32 K 0.0122 0.9044 0.0834 33 F 0.0156 0.8583 0.1261 34 S 0.0263 0.8064 0.1673 35 R 0.0051 0.9415 0.0533 36 K 0.0061 0.9470 0.0470 37 T 0.0070 0.9422 0.0508 38 I 0.0104 0.9237 0.0660 39 E 0.0158 0.8729 0.1114 40 H 0.0331 0.5378 0.4291 41 Q 0.0418 0.1507 0.8074 42 I 0.1148 0.0190 0.8662 43 P 0.0683 0.0101 0.9216 44 P 0.0062 0.9162 0.0776 45 E 0.0047 0.9496 0.0457 46 E 0.0054 0.9493 0.0453 47 I 0.0066 0.9515 0.0418 48 I 0.0067 0.9482 0.0451 49 S 0.0078 0.9401 0.0521 50 I 0.0108 0.9132 0.0761 51 H 0.0060 0.9309 0.0631 52 R 0.0047 0.9588 0.0365 53 K 0.0047 0.9604 0.0349 54 V 0.0047 0.9581 0.0371 55 L 0.0049 0.9521 0.0430 56 K 0.0052 0.9278 0.0670 57 E 0.0065 0.8316 0.1618 58 L 0.0125 0.6903 0.2971 59 Y 0.0448 0.3434 0.6118 60 P 0.0089 0.4021 0.5890 61 S 0.0146 0.2557 0.7297 62 L 0.0620 0.0448 0.8932 63 P 0.0370 0.1091 0.8540 64 E 0.0096 0.6866 0.3038 65 D 0.0123 0.7458 0.2419 66 V 0.0256 0.8442 0.1302 67 F 0.0320 0.8250 0.1430 68 H 0.0446 0.7928 0.1626 69 S 0.0133 0.9071 0.0796 70 L 0.0065 0.9453 0.0482 71 D 0.0054 0.9548 0.0398 72 F 0.0050 0.9587 0.0363 73 L 0.0047 0.9594 0.0359 74 I 0.0047 0.9600 0.0353 75 E 0.0047 0.9604 0.0349 76 V 0.0047 0.9576 0.0377 77 M 0.0053 0.9528 0.0418 78 I 0.0083 0.9374 0.0543 79 G 0.0132 0.9044 0.0825 80 Y 0.0194 0.8331 0.1474 81 G 0.0312 0.7732 0.1956 82 M 0.0498 0.7162 0.2340 83 A 0.0908 0.6666 0.2427 84 Y 0.0732 0.7203 0.2065 85 Q 0.0842 0.6967 0.2191 86 E 0.1122 0.6564 0.2314 87 H 0.0969 0.6935 0.2096 88 Q 0.0889 0.6610 0.2502 89 T 0.1023 0.6131 0.2846 90 L 0.0794 0.7069 0.2137 91 R 0.0459 0.7396 0.2145 92 G 0.0548 0.6062 0.3390 93 I 0.0355 0.7963 0.1682 94 Q 0.0273 0.8645 0.1083 95 Q 0.0153 0.9042 0.0805 96 E 0.0152 0.9153 0.0694 97 I 0.0088 0.9245 0.0667 98 K 0.0054 0.9274 0.0672 99 S 0.0065 0.9076 0.0859 100 E 0.0051 0.9443 0.0506 101 I 0.0051 0.9555 0.0394 102 E 0.0048 0.9565 0.0387 103 I 0.0052 0.9477 0.0471 104 A 0.0061 0.9290 0.0648 105 A 0.0061 0.8715 0.1224 106 N 0.0090 0.7443 0.2468 107 V 0.0239 0.6837 0.2924 108 Q 0.0414 0.5368 0.4218 109 Q 0.0602 0.3548 0.5850 110 T 0.0483 0.0829 0.8688