# This file is the result of combining several RDB files, specifically # T0209.t04.dssp-ebghstl.rdb (weight 1.53986) # T0209.t04.stride-ebghtl.rdb (weight 1.24869) # T0209.t04.str2.rdb (weight 1.54758) # T0209.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 T0209.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 12.8175 # # ============================================ # Comments from T0209.t04.stride-ebghtl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 12.8175 # # ============================================ # Comments from T0209.t04.str2.rdb # ============================================ # TARGET T0209 # 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 T0209.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 12.8175 # # ============================================ # Comments from T0209.t04.alpha.rdb # ============================================ # TARGET T0209 # 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 T0209.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 12.8175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.0940 0.1402 0.7658 2 A 0.1070 0.2213 0.6717 3 D 0.1006 0.2251 0.6744 4 S 0.0931 0.2262 0.6807 5 E 0.0744 0.0958 0.8298 6 P 0.0272 0.3184 0.6544 7 N 0.0459 0.2384 0.7157 8 A 0.0905 0.3896 0.5199 9 Q 0.0635 0.4553 0.4812 10 S 0.0597 0.5080 0.4323 11 S 0.0642 0.5096 0.4263 12 F 0.0850 0.5921 0.3229 13 A 0.0813 0.5873 0.3313 14 Q 0.0664 0.5780 0.3556 15 E 0.0764 0.4395 0.4841 16 K 0.1091 0.1712 0.7197 17 L 0.0834 0.0301 0.8865 18 P 0.1003 0.0376 0.8621 19 V 0.2257 0.0411 0.7333 20 K 0.5614 0.0259 0.4127 21 L 0.7777 0.0129 0.2094 22 T 0.8683 0.0087 0.1229 23 V 0.8647 0.0099 0.1255 24 E 0.7907 0.0121 0.1971 25 F 0.4302 0.0261 0.5437 26 T 0.1155 0.1084 0.7762 27 E 0.0075 0.8923 0.1001 28 Q 0.0053 0.9348 0.0599 29 A 0.0050 0.9438 0.0511 30 K 0.0050 0.9534 0.0416 31 S 0.0048 0.9517 0.0436 32 A 0.0049 0.9454 0.0497 33 V 0.0049 0.9417 0.0535 34 K 0.0053 0.9203 0.0744 35 K 0.0058 0.8820 0.1121 36 R 0.0077 0.8317 0.1606 37 E 0.0109 0.7144 0.2747 38 E 0.0132 0.6105 0.3763 39 K 0.0342 0.4005 0.5653 40 R 0.0632 0.1050 0.8318 41 P 0.0235 0.5031 0.4734 42 H 0.0273 0.6776 0.2951 43 L 0.0052 0.9330 0.0618 44 S 0.0048 0.9553 0.0399 45 R 0.0049 0.9595 0.0356 46 F 0.0056 0.9590 0.0354 47 I 0.0051 0.9603 0.0346 48 R 0.0049 0.9611 0.0340 49 Q 0.0047 0.9603 0.0350 50 V 0.0050 0.9533 0.0417 51 L 0.0063 0.9334 0.0603 52 E 0.0099 0.8320 0.1582 53 Q 0.0230 0.6765 0.3006 54 D 0.0913 0.1876 0.7211 55 P 0.0321 0.2576 0.7102 56 R 0.0641 0.1539 0.7820 57 P 0.0521 0.4143 0.5337 58 A 0.0448 0.5846 0.3706 59 Y 0.1028 0.4912 0.4060 60 Q 0.1531 0.2903 0.5565 61 Q 0.0816 0.1103 0.8082 62 G 0.0493 0.0457 0.9050 63 K 0.0824 0.0199 0.8977 64 P 0.0976 0.0472 0.8552 65 S 0.0840 0.1150 0.8010 66 D 0.1611 0.1036 0.7354 67 R 0.5453 0.0281 0.4266 68 I 0.8025 0.0093 0.1882 69 Y 0.8570 0.0143 0.1287 70 G 0.8872 0.0075 0.1054 71 M 0.8900 0.0056 0.1044 72 S 0.8895 0.0058 0.1047 73 L 0.8192 0.0289 0.1519 74 Y 0.7118 0.0588 0.2294 75 E 0.7245 0.0433 0.2322 76 F 0.7942 0.0115 0.1943 77 N 0.7987 0.0049 0.1964 78 V 0.8877 0.0038 0.1085 79 K 0.9084 0.0045 0.0871 80 W 0.9182 0.0035 0.0783 81 R 0.9155 0.0038 0.0808 82 I 0.8736 0.0047 0.1217 83 K 0.6631 0.0156 0.3213 84 A 0.2372 0.0474 0.7153 85 G 0.0728 0.0584 0.8688 86 T 0.1591 0.0566 0.7842 87 V 0.4854 0.0250 0.4897 88 N 0.5764 0.0323 0.3913 89 C 0.8955 0.0061 0.0984 90 V 0.9043 0.0041 0.0916 91 E 0.9198 0.0039 0.0763 92 V 0.9180 0.0037 0.0783 93 I 0.8508 0.0238 0.1253 94 E 0.8427 0.0111 0.1462 95 I 0.7628 0.0194 0.2179 96 E 0.6029 0.0285 0.3686 97 K 0.2954 0.0549 0.6497 98 D 0.1175 0.0389 0.8436 99 K 0.0680 0.0446 0.8875