# This file is the result of combining several RDB files, specifically # T0349.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0349.t2k.stride-ebghtl.rdb (weight 1.24869) # T0349.t2k.str2.rdb (weight 1.54758) # T0349.t2k.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 T0349.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0349 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0349.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31 # # ============================================ # Comments from T0349.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0349 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0349.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31 # # ============================================ # Comments from T0349.t2k.str2.rdb # ============================================ # TARGET T0349 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0349.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31 # # ============================================ # Comments from T0349.t2k.alpha.rdb # ============================================ # TARGET T0349 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0349.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1393 0.0816 0.7791 2 R 0.3330 0.1596 0.5074 3 E 0.5629 0.1294 0.3077 4 L 0.6030 0.1776 0.2195 5 L 0.6343 0.1394 0.2263 6 R 0.4534 0.1653 0.3813 7 T 0.1898 0.1210 0.6892 8 N 0.0506 0.0938 0.8556 9 D 0.0748 0.1307 0.7945 10 A 0.0434 0.8194 0.1372 11 V 0.0840 0.8478 0.0683 12 L 0.0527 0.9035 0.0438 13 L 0.0164 0.9429 0.0407 14 S 0.0084 0.9508 0.0408 15 A 0.0078 0.9521 0.0401 16 V 0.0053 0.9540 0.0407 17 G 0.0050 0.9522 0.0427 18 A 0.0052 0.9422 0.0526 19 L 0.0055 0.9236 0.0709 20 L 0.0069 0.8690 0.1241 21 D 0.0101 0.7114 0.2784 22 G 0.0192 0.4076 0.5732 23 A 0.0515 0.2628 0.6857 24 D 0.0596 0.0694 0.8710 25 I 0.1575 0.0206 0.8219 26 G 0.3107 0.0406 0.6487 27 H 0.8314 0.0134 0.1552 28 L 0.8877 0.0078 0.1044 29 V 0.8754 0.0100 0.1146 30 L 0.7726 0.0212 0.2062 31 D 0.3426 0.0360 0.6214 32 Q 0.0983 0.1597 0.7420 33 N 0.1082 0.1350 0.7568 34 M 0.1638 0.1682 0.6679 35 S 0.2486 0.1959 0.5554 36 I 0.2455 0.3555 0.3991 37 L 0.1643 0.3748 0.4609 38 E 0.1125 0.4162 0.4713 39 G 0.1123 0.2882 0.5995 40 S 0.1735 0.2364 0.5901 41 L 0.2022 0.2249 0.5728 42 G 0.2372 0.1571 0.6057 43 V 0.3000 0.1129 0.5870 44 I 0.2504 0.0523 0.6974 45 P 0.2822 0.0683 0.6495 46 R 0.4019 0.1104 0.4877 47 R 0.6573 0.0911 0.2516 48 V 0.6907 0.0850 0.2243 49 L 0.7381 0.0546 0.2073 50 V 0.4879 0.0528 0.4593 51 H 0.1494 0.0679 0.7826 52 E 0.0165 0.7052 0.2783 53 D 0.0085 0.7796 0.2119 54 D 0.0109 0.8210 0.1681 55 L 0.0049 0.9416 0.0535 56 A 0.0050 0.9499 0.0451 57 G 0.0048 0.9531 0.0421 58 A 0.0047 0.9587 0.0366 59 R 0.0047 0.9600 0.0353 60 R 0.0047 0.9597 0.0356 61 L 0.0047 0.9587 0.0366 62 L 0.0048 0.9555 0.0397 63 T 0.0050 0.9400 0.0550 64 D 0.0068 0.8944 0.0988 65 A 0.0442 0.5177 0.4381 66 G 0.0386 0.0810 0.8805 67 L 0.0525 0.0797 0.8678 68 A 0.0750 0.1867 0.7383 69 H 0.0832 0.5077 0.4092 70 E 0.1065 0.5074 0.3861 71 L 0.1302 0.3746 0.4953 72 R 0.1072 0.2288 0.6640 73 S 0.0667 0.2190 0.7143 74 D 0.0468 0.1619 0.7912 75 D 0.0420 0.0417 0.9163