# This file is the result of combining several RDB files, specifically # T0495.t04.dssp-ebghstl.rdb (weight 1.53986) # T0495.t04.stride-ebghtl.rdb (weight 1.24869) # T0495.t04.str2.rdb (weight 1.54758) # T0495.t04.alpha.rdb (weight 0.659012) # T0495.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0495.t2k.stride-ebghtl.rdb (weight 1.24869) # T0495.t2k.str2.rdb (weight 1.54758) # T0495.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 T0495.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.stride-ebghtl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 82 # # ============================================ # Comments from T0495.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 82 # # ============================================ # Comments from T0495.t2k.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 82 # # ============================================ # Comments from T0495.t2k.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 82 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0553 0.0261 0.9185 2 P 0.0844 0.0550 0.8607 3 M 0.0902 0.0966 0.8132 4 T 0.0300 0.3586 0.6114 5 L 0.0391 0.4205 0.5403 6 D 0.0599 0.4278 0.5123 7 L 0.0466 0.4757 0.4777 8 Q 0.0263 0.8091 0.1646 9 P 0.0071 0.9116 0.0813 10 G 0.0049 0.9485 0.0466 11 Q 0.0047 0.9568 0.0385 12 R 0.0047 0.9572 0.0381 13 L 0.0047 0.9553 0.0400 14 A 0.0048 0.9540 0.0412 15 R 0.0052 0.9416 0.0532 16 G 0.0049 0.9231 0.0720 17 V 0.0047 0.9507 0.0446 18 A 0.0047 0.9589 0.0365 19 R 0.0047 0.9596 0.0357 20 H 0.0047 0.9604 0.0350 21 L 0.0047 0.9579 0.0374 22 R 0.0050 0.9445 0.0505 23 A 0.0063 0.8705 0.1232 24 H 0.0430 0.3740 0.5829 25 G 0.0367 0.0261 0.9372 26 F 0.1573 0.0180 0.8248 27 V 0.6441 0.0096 0.3463 28 S 0.7821 0.0109 0.2070 29 V 0.7645 0.0205 0.2150 30 E 0.6969 0.0402 0.2629 31 E 0.6398 0.0322 0.3281 32 F 0.5853 0.0192 0.3954 33 V 0.5020 0.0180 0.4800 34 P 0.1461 0.0348 0.8191 35 A 0.0316 0.1321 0.8363 36 R 0.0421 0.0698 0.8881 37 G 0.0514 0.0525 0.8961 38 L 0.2219 0.0336 0.7445 39 R 0.5189 0.0167 0.4645 40 V 0.4387 0.0095 0.5517 41 D 0.5877 0.0234 0.3888 42 V 0.8637 0.0149 0.1214 43 M 0.8996 0.0105 0.0900 44 G 0.9064 0.0060 0.0876 45 L 0.8638 0.0063 0.1299 46 G 0.2071 0.0154 0.7775 47 P 0.0231 0.1132 0.8637 48 K 0.0571 0.0295 0.9134 49 G 0.1310 0.0288 0.8402 50 E 0.4628 0.0077 0.5295 51 I 0.8925 0.0032 0.1043 52 W 0.9233 0.0053 0.0714 53 V 0.9303 0.0036 0.0661 54 I 0.9268 0.0039 0.0693 55 E 0.9115 0.0049 0.0836 56 C 0.8297 0.0073 0.1630 57 K 0.6087 0.0221 0.3692 58 S 0.2536 0.0220 0.7244 59 S 0.0944 0.0212 0.8844 60 R 0.0076 0.8385 0.1539 61 A 0.0065 0.8910 0.1026 62 D 0.0166 0.8807 0.1027 63 F 0.0127 0.8597 0.1276 64 Q 0.0272 0.7757 0.1971 65 A 0.0275 0.6236 0.3489 66 D 0.0390 0.4114 0.5496 67 A 0.0313 0.4241 0.5446 68 K 0.0371 0.3748 0.5880 69 W 0.0329 0.3883 0.5788 70 Q 0.0146 0.6258 0.3595 71 G 0.0202 0.5916 0.3883 72 Y 0.0304 0.6148 0.3548 73 L 0.0333 0.6228 0.3439 74 E 0.0226 0.5863 0.3911 75 W 0.0417 0.5444 0.4139 76 C 0.1132 0.4133 0.4735 77 D 0.1813 0.3122 0.5065 78 R 0.3652 0.2701 0.3647 79 Y 0.5640 0.2044 0.2316 80 F 0.6452 0.1334 0.2214 81 W 0.6714 0.0808 0.2478 82 A 0.4651 0.0442 0.4907 83 V 0.2060 0.0276 0.7663 84 D 0.0854 0.0697 0.8448 85 M 0.0260 0.2427 0.7313 86 E 0.0364 0.2069 0.7567 87 F 0.0979 0.0658 0.8362 88 P 0.1266 0.1011 0.7723 89 A 0.0342 0.6842 0.2815 90 E 0.0195 0.7066 0.2739 91 L 0.0513 0.5650 0.3837 92 L 0.1284 0.0635 0.8081 93 P 0.0657 0.1121 0.8222 94 A 0.0322 0.2523 0.7155 95 E 0.0571 0.2212 0.7217 96 S 0.3231 0.0513 0.6256 97 G 0.6326 0.0256 0.3418 98 L 0.8917 0.0092 0.0991 99 L 0.9074 0.0089 0.0837 100 I 0.9011 0.0078 0.0912 101 A 0.8251 0.0129 0.1620 102 D 0.4422 0.0198 0.5380 103 A 0.0912 0.1345 0.7743 104 Y 0.0600 0.0863 0.8537 105 D 0.1443 0.0824 0.7732 106 A 0.5780 0.0328 0.3892 107 E 0.8503 0.0154 0.1343 108 I 0.8724 0.0171 0.1105 109 V 0.7752 0.0343 0.1905 110 R 0.5566 0.0574 0.3860 111 M 0.2400 0.0697 0.6902 112 A 0.1136 0.0459 0.8405 113 P 0.0828 0.1370 0.7802 114 E 0.0512 0.2796 0.6692 115 Q 0.0671 0.2538 0.6791 116 K 0.0492 0.2053 0.7455 117 L 0.0483 0.1713 0.7805 118 A 0.0293 0.3600 0.6107 119 P 0.0167 0.7655 0.2178 120 A 0.0106 0.9034 0.0860 121 R 0.0086 0.9324 0.0590 122 R 0.0068 0.9439 0.0493 123 K 0.0055 0.9543 0.0401 124 V 0.0047 0.9578 0.0375 125 L 0.0047 0.9586 0.0367 126 I 0.0047 0.9595 0.0358 127 Q 0.0047 0.9606 0.0347 128 K 0.0047 0.9605 0.0348 129 F 0.0047 0.9603 0.0351 130 A 0.0047 0.9604 0.0349 131 T 0.0047 0.9604 0.0349 132 H 0.0048 0.9590 0.0363 133 A 0.0047 0.9570 0.0383 134 A 0.0048 0.9533 0.0420 135 R 0.0049 0.9472 0.0479 136 R 0.0051 0.9365 0.0585 137 L 0.0077 0.9237 0.0687 138 Q 0.0065 0.8961 0.0974 139 A 0.0107 0.8595 0.1298 140 L 0.0161 0.7435 0.2404 141 R 0.0408 0.5179 0.4414 142 D 0.0774 0.0766 0.8460 143 P 0.0159 0.2928 0.6914 144 E 0.0191 0.2330 0.7479 145 G 0.0547 0.2653 0.6800 146 H 0.0996 0.1702 0.7302 147 G 0.1222 0.1910 0.6869 148 I 0.1176 0.1585 0.7238 149 F 0.0856 0.0957 0.8187 150 E 0.0377 0.0497 0.9126