# This file is the result of combining several RDB files, specifically # T0335.t04.dssp-ebghstl.rdb (weight 1.53986) # T0335.t04.stride-ebghtl.rdb (weight 1.24869) # T0335.t04.str2.rdb (weight 1.54758) # T0335.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 T0335.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 10.373 # # ============================================ # Comments from T0335.t04.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 10.373 # # ============================================ # Comments from T0335.t04.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 10.373 # # ============================================ # Comments from T0335.t04.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 10.373 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0516 0.1862 0.7622 2 I 0.0646 0.2945 0.6409 3 S 0.0366 0.5015 0.4618 4 N 0.0109 0.8443 0.1448 5 A 0.0080 0.9085 0.0835 6 K 0.0052 0.9395 0.0553 7 I 0.0047 0.9490 0.0463 8 A 0.0047 0.9522 0.0431 9 R 0.0047 0.9535 0.0418 10 I 0.0047 0.9566 0.0387 11 N 0.0047 0.9573 0.0381 12 E 0.0047 0.9555 0.0398 13 L 0.0047 0.9464 0.0489 14 A 0.0048 0.9250 0.0702 15 A 0.0049 0.8853 0.1098 16 K 0.0071 0.8453 0.1476 17 A 0.0165 0.7952 0.1883 18 K 0.0171 0.7369 0.2460 19 A 0.0334 0.5681 0.3985 20 G 0.0338 0.1735 0.7927 21 V 0.0607 0.0836 0.8557 22 I 0.1358 0.0194 0.8448 23 T 0.0625 0.0203 0.9172 24 E 0.0048 0.9434 0.0518 25 E 0.0047 0.9523 0.0430 26 E 0.0048 0.9562 0.0391 27 K 0.0047 0.9590 0.0363 28 A 0.0046 0.9589 0.0365 29 E 0.0046 0.9549 0.0405 30 Q 0.0047 0.9565 0.0389 31 Q 0.0046 0.9574 0.0380 32 K 0.0047 0.9527 0.0427 33 L 0.0047 0.9496 0.0457 34 R 0.0047 0.9574 0.0379 35 Q 0.0047 0.9598 0.0355 36 E 0.0049 0.9557 0.0393 37 Y 0.0048 0.9517 0.0435 38 L 0.0048 0.9549 0.0404 39 K 0.0049 0.9528 0.0423 40 G 0.0049 0.9441 0.0511 41 F 0.0050 0.9378 0.0571 42 R 0.0053 0.9490 0.0457 43 S 0.0051 0.9463 0.0486 44 S 0.0053 0.9345 0.0602 45 M 0.0054 0.9342 0.0604 46 K 0.0065 0.9201 0.0733 47 N 0.0103 0.8553 0.1344 48 T 0.0204 0.7328 0.2468 49 L 0.1030 0.5305 0.3666 50 K 0.1330 0.3604 0.5065 51 S 0.2365 0.2173 0.5462 52 V 0.6277 0.0456 0.3267 53 K 0.8143 0.0201 0.1655 54 I 0.8766 0.0085 0.1149 55 I 0.7734 0.0134 0.2131 56 D 0.1698 0.0143 0.8159 57 P 0.0114 0.1251 0.8635 58 E 0.0389 0.0438 0.9173 59 G 0.0566 0.0540 0.8894 60 N 0.0876 0.0783 0.8341 61 D 0.3046 0.0793 0.6160 62 V 0.2396 0.0463 0.7142 63 T 0.0897 0.0308 0.8795 64 P 0.0082 0.9031 0.0887 65 E 0.0048 0.9424 0.0528 66 K 0.0047 0.9476 0.0476 67 L 0.0056 0.9383 0.0561 68 K 0.0057 0.9327 0.0616 69 R 0.0054 0.9382 0.0564 70 E 0.0058 0.9268 0.0674 71 Q 0.0088 0.8901 0.1011 72 R 0.0128 0.8335 0.1538 73 N 0.0149 0.6949 0.2902 74 N 0.0392 0.3992 0.5616 75 K 0.0450 0.2459 0.7091 76 L 0.0726 0.1062 0.8212 77 H 0.0512 0.0438 0.9050