# This file is the result of combining several RDB files, specifically # T0345.t06.dssp-ebghstl.rdb (weight 1.53986) # T0345.t06.stride-ebghtl.rdb (weight 1.24869) # T0345.t06.str2.rdb (weight 1.54758) # T0345.t06.alpha.rdb (weight 0.659012) # T0345.t04.dssp-ebghstl.rdb (weight 1.53986) # T0345.t04.stride-ebghtl.rdb (weight 1.24869) # T0345.t04.str2.rdb (weight 1.54758) # T0345.t04.alpha.rdb (weight 0.659012) # T0345.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0345.t2k.stride-ebghtl.rdb (weight 1.24869) # T0345.t2k.str2.rdb (weight 1.54758) # T0345.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 T0345.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.stride-ebghtl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.str2.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.alpha.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.stride-ebghtl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.str2.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.alpha.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 547 # # ============================================ # Comments from T0345.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 547 # # ============================================ # Comments from T0345.t2k.str2.rdb # ============================================ # TARGET T0345 # 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 T0345.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 547 # # ============================================ # Comments from T0345.t2k.alpha.rdb # ============================================ # TARGET T0345 # 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 T0345.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 547 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0999 0.1182 0.7819 2 I 0.2453 0.1523 0.6024 3 A 0.2134 0.1588 0.6278 4 K 0.2354 0.1216 0.6430 5 S 0.3009 0.0804 0.6187 6 F 0.2287 0.1464 0.6249 7 Y 0.2329 0.1401 0.6271 8 D 0.3493 0.0975 0.5532 9 L 0.5293 0.0232 0.4475 10 S 0.6964 0.0098 0.2939 11 A 0.7693 0.0103 0.2204 12 I 0.7767 0.0175 0.2059 13 N 0.3662 0.0171 0.6167 14 L 0.0596 0.1174 0.8229 15 D 0.0510 0.0216 0.9274 16 G 0.0403 0.0340 0.9257 17 E 0.2704 0.0114 0.7182 18 K 0.8121 0.0049 0.1830 19 V 0.7477 0.0061 0.2462 20 D 0.5255 0.0134 0.4611 21 F 0.0365 0.6880 0.2756 22 N 0.0139 0.7315 0.2546 23 T 0.0255 0.7206 0.2539 24 F 0.0996 0.3624 0.5380 25 R 0.0706 0.1194 0.8100 26 G 0.0873 0.0383 0.8744 27 R 0.3555 0.0133 0.6312 28 A 0.6642 0.0044 0.3314 29 V 0.8766 0.0090 0.1143 30 L 0.9274 0.0042 0.0684 31 I 0.9195 0.0069 0.0736 32 E 0.8373 0.0252 0.1375 33 N 0.5748 0.0310 0.3942 34 V 0.2669 0.1136 0.6195 35 A 0.2029 0.2043 0.5929 36 S 0.1100 0.3429 0.5471 37 L 0.0893 0.2954 0.6153 38 C 0.0832 0.1796 0.7371 39 G 0.0605 0.1231 0.8164 40 T 0.0711 0.1205 0.8085 41 T 0.0647 0.1109 0.8244 42 T 0.0318 0.3227 0.6456 43 R 0.0366 0.3150 0.6483 44 D 0.0205 0.5160 0.4635 45 F 0.0077 0.8773 0.1150 46 T 0.0072 0.8944 0.0984 47 Q 0.0051 0.9460 0.0489 48 L 0.0053 0.9508 0.0439 49 N 0.0048 0.9537 0.0415 50 E 0.0048 0.9515 0.0437 51 L 0.0052 0.9408 0.0540 52 Q 0.0056 0.9291 0.0653 53 C 0.0090 0.8806 0.1104 54 R 0.0378 0.7507 0.2115 55 F 0.0222 0.5819 0.3959 56 P 0.0166 0.4210 0.5623 57 R 0.0552 0.1551 0.7898 58 R 0.0887 0.0395 0.8718 59 L 0.4676 0.0065 0.5259 60 V 0.8743 0.0040 0.1217 61 V 0.9194 0.0034 0.0771 62 L 0.8750 0.0123 0.1127 63 G 0.8442 0.0079 0.1479 64 F 0.6493 0.0145 0.3362 65 P 0.4353 0.0222 0.5424 66 C 0.1841 0.1143 0.7016 67 N 0.0994 0.1974 0.7033 68 Q 0.0707 0.2652 0.6641 69 F 0.0728 0.2119 0.7153 70 G 0.0704 0.1612 0.7683 71 H 0.0796 0.1188 0.8017 72 Q 0.1474 0.0959 0.7567 73 E 0.1029 0.0512 0.8459 74 N 0.0716 0.0836 0.8448 75 C 0.0710 0.0790 0.8500 76 Q 0.0552 0.1131 0.8316 77 N 0.0089 0.8861 0.1050 78 E 0.0064 0.9294 0.0642 79 E 0.0060 0.9411 0.0529 80 I 0.0056 0.9493 0.0451 81 L 0.0081 0.9378 0.0541 82 N 0.0070 0.9201 0.0728 83 S 0.0112 0.8509 0.1380 84 L 0.0401 0.7445 0.2154 85 K 0.0697 0.6996 0.2307 86 Y 0.1090 0.5264 0.3646 87 V 0.1611 0.2417 0.5972 88 R 0.0969 0.0551 0.8481 89 P 0.0498 0.1291 0.8211 90 G 0.0376 0.1274 0.8350 91 G 0.0582 0.1190 0.8228 92 G 0.1063 0.0784 0.8153 93 Y 0.1945 0.0693 0.7362 94 Q 0.2003 0.0482 0.7514 95 P 0.2671 0.0318 0.7011 96 T 0.3170 0.0357 0.6473 97 F 0.3848 0.0261 0.5891 98 T 0.4365 0.0424 0.5211 99 L 0.4156 0.1165 0.4679 100 V 0.5094 0.1234 0.3673 101 Q 0.5212 0.0915 0.3872 102 K 0.5650 0.0629 0.3721 103 C 0.6344 0.0290 0.3366 104 E 0.5785 0.0234 0.3981 105 V 0.4290 0.0401 0.5309 106 N 0.1544 0.0497 0.7959 107 G 0.0529 0.0843 0.8628 108 Q 0.0293 0.1933 0.7774 109 N 0.0411 0.1923 0.7666 110 E 0.0585 0.2724 0.6691 111 H 0.0534 0.3287 0.6179 112 P 0.0319 0.8335 0.1346 113 V 0.0103 0.9151 0.0746 114 F 0.0064 0.9444 0.0492 115 A 0.0059 0.9492 0.0449 116 Y 0.0052 0.9430 0.0518 117 L 0.0070 0.9303 0.0627 118 K 0.0080 0.8958 0.0962 119 D 0.0140 0.7985 0.1875 120 K 0.0333 0.6130 0.3538 121 L 0.0655 0.2065 0.7280 122 P 0.0542 0.1643 0.7815 123 Y 0.0740 0.1627 0.7633 124 P 0.0891 0.1649 0.7460 125 Y 0.0827 0.1354 0.7820 126 D 0.0731 0.1040 0.8229 127 D 0.0961 0.0946 0.8093 128 P 0.0533 0.2867 0.6599 129 F 0.0628 0.3208 0.6164 130 S 0.0828 0.3789 0.5383 131 L 0.1284 0.3471 0.5245 132 M 0.1426 0.2599 0.5975 133 T 0.1240 0.1808 0.6952 134 D 0.1178 0.1313 0.7509 135 P 0.0532 0.4694 0.4774 136 K 0.0508 0.5021 0.4472 137 L 0.0750 0.4947 0.4303 138 I 0.1534 0.3336 0.5131 139 I 0.2176 0.2159 0.5665 140 W 0.2254 0.1882 0.5865 141 S 0.1845 0.1657 0.6498 142 P 0.1876 0.1986 0.6138 143 V 0.2054 0.1572 0.6374 144 R 0.1789 0.1188 0.7022 145 R 0.1105 0.1992 0.6902 146 S 0.0899 0.1685 0.7416 147 D 0.1642 0.1128 0.7230 148 V 0.3810 0.0533 0.5657 149 A 0.4579 0.0489 0.4932 150 W 0.5404 0.0457 0.4138 151 N 0.4372 0.0408 0.5220 152 F 0.4224 0.0880 0.4896 153 E 0.5524 0.0876 0.3599 154 K 0.7386 0.0612 0.2002 155 F 0.7972 0.0258 0.1770 156 L 0.8098 0.0187 0.1715 157 I 0.8017 0.0113 0.1870 158 G 0.1693 0.0153 0.8154 159 P 0.0182 0.1115 0.8703 160 E 0.0510 0.0177 0.9313 161 G 0.0795 0.0221 0.8985 162 E 0.2780 0.0091 0.7129 163 P 0.8565 0.0034 0.1401 164 F 0.8281 0.0165 0.1554 165 R 0.8276 0.0106 0.1618 166 R 0.7248 0.0270 0.2482 167 Y 0.5812 0.0276 0.3913 168 S 0.2813 0.0306 0.6881 169 R 0.0687 0.0769 0.8544 170 T 0.0748 0.0667 0.8586 171 F 0.1356 0.0300 0.8344 172 P 0.0837 0.0254 0.8909 173 T 0.0260 0.6851 0.2889 174 I 0.0095 0.7603 0.2302 175 N 0.0142 0.7998 0.1860 176 I 0.0098 0.8375 0.1527 177 E 0.0056 0.9132 0.0811 178 P 0.0053 0.9280 0.0667 179 D 0.0051 0.9413 0.0535 180 I 0.0049 0.9447 0.0504 181 K 0.0049 0.9409 0.0542 182 R 0.0058 0.9082 0.0860 183 L 0.0088 0.7858 0.2054 184 L 0.0537 0.5292 0.4171 185 K 0.0283 0.1533 0.8184