# This file is the result of combining several RDB files, specifically # T0363.t06.dssp-ebghstl.rdb (weight 1.53986) # T0363.t06.stride-ebghtl.rdb (weight 1.24869) # T0363.t06.str2.rdb (weight 1.54758) # T0363.t06.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 T0363.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0363 # 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 T0363.t06-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 16.2742 # # ============================================ # Comments from T0363.t06.stride-ebghtl.rdb # ============================================ # TARGET T0363 # Using neural net t06-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 T0363.t06-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 16.2742 # # ============================================ # Comments from T0363.t06.str2.rdb # ============================================ # TARGET T0363 # Using neural net t06-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 T0363.t06-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 16.2742 # # ============================================ # Comments from T0363.t06.alpha.rdb # ============================================ # TARGET T0363 # Using neural net t06-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 T0363.t06-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 16.2742 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0788 0.1575 0.7637 2 A 0.1346 0.2191 0.6463 3 H 0.1547 0.2282 0.6171 4 H 0.1364 0.2067 0.6568 5 H 0.1426 0.2054 0.6520 6 H 0.1937 0.1710 0.6353 7 H 0.2126 0.1706 0.6168 8 H 0.2234 0.1462 0.6304 9 S 0.2413 0.1369 0.6218 10 L 0.1923 0.2003 0.6074 11 N 0.2087 0.1447 0.6467 12 Q 0.5469 0.0563 0.3968 13 I 0.7910 0.0050 0.2040 14 N 0.9042 0.0035 0.0924 15 I 0.9162 0.0034 0.0804 16 E 0.9205 0.0035 0.0760 17 I 0.9278 0.0032 0.0690 18 A 0.9189 0.0043 0.0767 19 Y 0.9035 0.0045 0.0920 20 A 0.7208 0.0096 0.2696 21 F 0.3231 0.0156 0.6613 22 P 0.1141 0.0881 0.7978 23 E 0.0738 0.1571 0.7691 24 R 0.2405 0.1575 0.6020 25 Y 0.5813 0.0436 0.3751 26 Y 0.8038 0.0156 0.1806 27 L 0.8764 0.0057 0.1179 28 K 0.8503 0.0173 0.1323 29 S 0.8937 0.0061 0.1002 30 F 0.8799 0.0052 0.1149 31 Q 0.8614 0.0053 0.1333 32 V 0.5348 0.0118 0.4534 33 D 0.1497 0.0204 0.8299 34 E 0.0227 0.0945 0.8828 35 G 0.0277 0.0398 0.9325 36 I 0.1936 0.0220 0.7843 37 T 0.2698 0.0348 0.6954 38 V 0.0060 0.9516 0.0424 39 Q 0.0047 0.9604 0.0350 40 T 0.0047 0.9602 0.0351 41 A 0.0047 0.9606 0.0347 42 I 0.0047 0.9588 0.0365 43 T 0.0049 0.9410 0.0541 44 Q 0.0052 0.8895 0.1053 45 S 0.0435 0.6009 0.3556 46 G 0.0216 0.2391 0.7393 47 I 0.0331 0.4954 0.4715 48 L 0.0377 0.6577 0.3046 49 S 0.0404 0.5772 0.3824 50 Q 0.0581 0.4334 0.5086 51 F 0.0881 0.0620 0.8499 52 P 0.0508 0.1730 0.7762 53 E 0.0989 0.2029 0.6982 54 I 0.2566 0.0995 0.6439 55 D 0.2103 0.0421 0.7476 56 L 0.0523 0.4195 0.5282 57 S 0.0489 0.3072 0.6439 58 T 0.0706 0.2830 0.6463 59 N 0.2113 0.0571 0.7316 60 K 0.5245 0.0419 0.4336 61 I 0.7870 0.0206 0.1924 62 G 0.8208 0.0159 0.1633 63 I 0.8297 0.0175 0.1528 64 F 0.6767 0.0268 0.2965 65 S 0.4339 0.0297 0.5364 66 R 0.4573 0.0166 0.5261 67 P 0.5105 0.0183 0.4711 68 I 0.4801 0.0201 0.4999 69 K 0.3679 0.0202 0.6119 70 L 0.0946 0.3862 0.5192 71 T 0.0620 0.4502 0.4878 72 D 0.1229 0.3156 0.5615 73 V 0.2790 0.2276 0.4934 74 L 0.2651 0.1717 0.5633 75 K 0.1038 0.1119 0.7843 76 E 0.0386 0.1084 0.8530 77 G 0.0276 0.0439 0.9285 78 D 0.1162 0.0222 0.8616 79 R 0.7250 0.0100 0.2650 80 I 0.8927 0.0084 0.0989 81 E 0.9014 0.0138 0.0847 82 I 0.8815 0.0158 0.1027 83 Y 0.7771 0.0288 0.1940 84 R 0.5314 0.0739 0.3948 85 P 0.3276 0.1640 0.5084 86 L 0.2700 0.2159 0.5141 87 L 0.3136 0.1412 0.5451 88 A 0.2007 0.0870 0.7124 89 D 0.1185 0.0366 0.8448 90 P 0.0120 0.8074 0.1806 91 K 0.0084 0.8893 0.1023 92 E 0.0133 0.9064 0.0803 93 I 0.0202 0.8919 0.0879 94 R 0.0402 0.8259 0.1339 95 R 0.0512 0.6456 0.3031 96 E 0.0454 0.2238 0.7308 97 G 0.0349 0.0253 0.9398