# This file is the result of combining several RDB files, specifically # T0330.t06.dssp-ebghstl.rdb (weight 1.53986) # T0330.t06.stride-ebghtl.rdb (weight 1.24869) # T0330.t06.str2.rdb (weight 1.54758) # T0330.t06.alpha.rdb (weight 0.659012) # T0330.t04.dssp-ebghstl.rdb (weight 1.53986) # T0330.t04.stride-ebghtl.rdb (weight 1.24869) # T0330.t04.str2.rdb (weight 1.54758) # T0330.t04.alpha.rdb (weight 0.659012) # T0330.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0330.t2k.stride-ebghtl.rdb (weight 1.24869) # T0330.t2k.str2.rdb (weight 1.54758) # T0330.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 T0330.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ # Comments from T0330.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 784 # # ============================================ # Comments from T0330.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 784 # # ============================================ # Comments from T0330.t2k.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 784 # # ============================================ # Comments from T0330.t2k.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 784 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0815 0.0235 0.8950 2 S 0.2094 0.0155 0.7751 3 R 0.4056 0.0116 0.5828 4 T 0.6872 0.0235 0.2893 5 L 0.8942 0.0047 0.1011 6 V 0.9232 0.0039 0.0730 7 L 0.9159 0.0047 0.0794 8 F 0.8719 0.0076 0.1205 9 D 0.5427 0.0166 0.4407 10 I 0.1677 0.1242 0.7081 11 D 0.1101 0.0689 0.8210 12 G 0.1502 0.1056 0.7443 13 T 0.3109 0.0991 0.5899 14 L 0.4605 0.1386 0.4009 15 L 0.3260 0.1616 0.5124 16 K 0.1855 0.1117 0.7028 17 V 0.0491 0.3308 0.6201 18 E 0.0301 0.8204 0.1494 19 S 0.0062 0.9308 0.0629 20 M 0.0057 0.9381 0.0563 21 N 0.0049 0.9466 0.0485 22 R 0.0048 0.9529 0.0423 23 R 0.0048 0.9559 0.0394 24 V 0.0047 0.9572 0.0381 25 L 0.0047 0.9578 0.0375 26 A 0.0047 0.9576 0.0377 27 D 0.0048 0.9558 0.0394 28 A 0.0047 0.9556 0.0396 29 L 0.0049 0.9461 0.0489 30 I 0.0053 0.9270 0.0677 31 E 0.0071 0.8569 0.1359 32 V 0.0432 0.4879 0.4689 33 Y 0.0381 0.0710 0.8909 34 G 0.0582 0.0410 0.9008 35 T 0.0835 0.0503 0.8662 36 E 0.0831 0.1072 0.8097 37 G 0.0723 0.1149 0.8128 38 S 0.0517 0.4361 0.5121 39 T 0.0095 0.8664 0.1241 40 G 0.0106 0.8865 0.1029 41 S 0.0124 0.8998 0.0879 42 H 0.0155 0.8938 0.0907 43 D 0.0166 0.8738 0.1096 44 F 0.0201 0.8184 0.1615 45 S 0.0414 0.6362 0.3224 46 G 0.0581 0.3742 0.5677 47 K 0.0504 0.2135 0.7361 48 M 0.0413 0.2670 0.6917 49 D 0.0370 0.4187 0.5443 50 G 0.0131 0.8483 0.1386 51 A 0.0080 0.9163 0.0757 52 I 0.0088 0.9319 0.0593 53 I 0.0084 0.9392 0.0524 54 Y 0.0111 0.9374 0.0516 55 E 0.0113 0.9323 0.0564 56 V 0.0103 0.9192 0.0705 57 L 0.0132 0.8816 0.1052 58 S 0.0146 0.8376 0.1477 59 N 0.0155 0.7519 0.2326 60 V 0.0309 0.6078 0.3614 61 G 0.0435 0.4249 0.5316 62 L 0.0486 0.3677 0.5837 63 E 0.0494 0.3638 0.5868 64 R 0.0572 0.3133 0.6295 65 A 0.0355 0.4318 0.5327 66 E 0.0397 0.4197 0.5406 67 I 0.0346 0.4449 0.5205 68 A 0.0381 0.4259 0.5360 69 D 0.0218 0.6732 0.3051 70 K 0.0119 0.7426 0.2455 71 F 0.0125 0.7558 0.2317 72 D 0.0077 0.8494 0.1428 73 K 0.0065 0.9004 0.0931 74 A 0.0059 0.9151 0.0790 75 K 0.0061 0.9145 0.0794 76 E 0.0056 0.9260 0.0685 77 T 0.0055 0.9284 0.0661 78 Y 0.0054 0.9300 0.0646 79 I 0.0056 0.9241 0.0703 80 A 0.0054 0.9310 0.0636 81 L 0.0053 0.9345 0.0602 82 F 0.0055 0.9310 0.0634 83 R 0.0063 0.9235 0.0702 84 E 0.0064 0.9092 0.0844 85 R 0.0076 0.8785 0.1138 86 A 0.0120 0.8020 0.1860 87 R 0.0210 0.6426 0.3364 88 R 0.0255 0.5184 0.4561 89 E 0.0265 0.4298 0.5436 90 D 0.0392 0.2795 0.6813 91 I 0.0811 0.1294 0.7895 92 T 0.0950 0.1234 0.7816 93 L 0.1174 0.1101 0.7724 94 L 0.0719 0.0881 0.8400 95 E 0.0195 0.4052 0.5752 96 G 0.0300 0.4067 0.5633 97 V 0.0102 0.9037 0.0861 98 R 0.0048 0.9541 0.0411 99 E 0.0048 0.9563 0.0389 100 L 0.0047 0.9577 0.0375 101 L 0.0048 0.9561 0.0391 102 D 0.0048 0.9532 0.0420 103 A 0.0050 0.9444 0.0506 104 L 0.0057 0.9308 0.0634 105 S 0.0055 0.9071 0.0874 106 S 0.0073 0.8174 0.1752 107 R 0.0343 0.5925 0.3732 108 S 0.0438 0.1881 0.7681 109 D 0.0376 0.0378 0.9246 110 V 0.1032 0.0112 0.8856 111 L 0.3259 0.0120 0.6622 112 L 0.9018 0.0045 0.0937 113 G 0.9248 0.0036 0.0716 114 L 0.9274 0.0033 0.0693 115 L 0.8774 0.0077 0.1149 116 T 0.4631 0.0245 0.5123 117 G 0.0693 0.0326 0.8981 118 N 0.0615 0.0579 0.8806 119 F 0.0568 0.3348 0.6084 120 E 0.0176 0.8066 0.1759 121 A 0.0079 0.9005 0.0916 122 S 0.0068 0.9209 0.0723 123 G 0.0049 0.9477 0.0474 124 R 0.0051 0.9565 0.0385 125 H 0.0050 0.9582 0.0369 126 K 0.0047 0.9581 0.0372 127 L 0.0048 0.9546 0.0406 128 K 0.0052 0.9396 0.0553 129 L 0.0063 0.8763 0.1174 130 P 0.0435 0.4010 0.5555 131 G 0.0496 0.0518 0.8986 132 I 0.0702 0.1205 0.8092 133 D 0.0699 0.3439 0.5862 134 H 0.0699 0.4751 0.4550 135 Y 0.1692 0.3511 0.4797 136 F 0.2818 0.0933 0.6249 137 P 0.3541 0.0981 0.5478 138 F 0.8158 0.0380 0.1462 139 G 0.8754 0.0238 0.1008 140 A 0.8515 0.0241 0.1243 141 F 0.5634 0.0383 0.3983 142 A 0.1567 0.1535 0.6898 143 D 0.0743 0.2445 0.6812 144 D 0.0816 0.3229 0.5955 145 A 0.0938 0.3161 0.5902 146 L 0.0620 0.2929 0.6451 147 D 0.0624 0.2164 0.7212 148 R 0.0659 0.1271 0.8070 149 N 0.0753 0.1226 0.8021 150 E 0.0794 0.1230 0.7976 151 L 0.0790 0.1119 0.8091 152 P 0.0225 0.6057 0.3718 153 H 0.0119 0.8354 0.1526 154 I 0.0061 0.9257 0.0682 155 A 0.0050 0.9476 0.0474 156 L 0.0050 0.9526 0.0424 157 E 0.0047 0.9529 0.0423 158 R 0.0048 0.9505 0.0447 159 A 0.0048 0.9445 0.0507 160 R 0.0049 0.9204 0.0747 161 R 0.0057 0.8680 0.1263 162 M 0.0109 0.7634 0.2258 163 T 0.0256 0.6286 0.3458 164 G 0.0297 0.4181 0.5522 165 A 0.0528 0.2543 0.6929 166 N 0.0540 0.0713 0.8747 167 Y 0.0855 0.0180 0.8965 168 S 0.0751 0.0156 0.9093 169 P 0.0368 0.5336 0.4296 170 S 0.0365 0.5372 0.4263 171 Q 0.1951 0.4048 0.4001 172 I 0.7503 0.0258 0.2239 173 V 0.8505 0.0127 0.1368 174 I 0.8977 0.0072 0.0952 175 I 0.7834 0.0427 0.1739 176 G 0.4576 0.0298 0.5125 177 D 0.1515 0.0227 0.8259 178 T 0.0602 0.0364 0.9034 179 E 0.0102 0.7030 0.2869 180 H 0.0074 0.8243 0.1683 181 D 0.0067 0.8984 0.0949 182 I 0.0058 0.9536 0.0406 183 R 0.0050 0.9557 0.0393 184 C 0.0048 0.9582 0.0370 185 A 0.0047 0.9569 0.0383 186 R 0.0049 0.9481 0.0470 187 E 0.0063 0.9041 0.0897 188 L 0.0419 0.3850 0.5732 189 D 0.0488 0.0153 0.9359 190 A 0.0949 0.0075 0.8976 191 R 0.4689 0.0237 0.5075 192 S 0.9200 0.0038 0.0762 193 I 0.9259 0.0044 0.0697 194 A 0.9254 0.0038 0.0708 195 V 0.8905 0.0067 0.1028 196 A 0.6852 0.0224 0.2924 197 T 0.2101 0.0442 0.7457 198 G 0.0873 0.0653 0.8474 199 N 0.0896 0.0954 0.8150 200 F 0.1040 0.0760 0.8200 201 T 0.0707 0.1192 0.8101 202 M 0.0141 0.7800 0.2058 203 E 0.0088 0.8464 0.1448 204 E 0.0068 0.8900 0.1032 205 L 0.0071 0.8896 0.1033 206 A 0.0087 0.8562 0.1351 207 R 0.0134 0.7400 0.2466 208 H 0.0510 0.4502 0.4988 209 K 0.0829 0.0867 0.8304 210 P 0.0922 0.0541 0.8536 211 G 0.2058 0.1064 0.6879 212 T 0.8087 0.0339 0.1574 213 L 0.8713 0.0177 0.1110 214 F 0.7644 0.0226 0.2130 215 K 0.2377 0.0809 0.6814 216 N 0.1053 0.0212 0.8736 217 F 0.0096 0.7375 0.2529 218 A 0.0057 0.8717 0.1226 219 E 0.0081 0.8842 0.1078 220 T 0.0056 0.9321 0.0623 221 D 0.0050 0.9454 0.0497 222 E 0.0051 0.9382 0.0567 223 V 0.0064 0.9294 0.0642 224 L 0.0093 0.9047 0.0861 225 A 0.0072 0.8461 0.1467 226 S 0.0115 0.7141 0.2744 227 I 0.0222 0.5933 0.3845 228 L 0.0605 0.3349 0.6046 229 T 0.0530 0.1448 0.8022 230 P 0.0393 0.3542 0.6066 231 K 0.0571 0.3182 0.6247 232 H 0.0770 0.2291 0.6938 233 S 0.0470 0.0682 0.8847