# This file is the result of combining several RDB files, specifically # T0191.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0191.t2k.stride-ebghtl.rdb (weight 1.24869) # T0191.t2k.str.rdb (weight 1.53983) # T0191.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 T0191.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0191 # 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 T0191.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 188 # # ============================================ # Comments from T0191.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0191 # 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 T0191.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 188 # # ============================================ # Comments from T0191.t2k.str.rdb # ============================================ # TARGET T0191 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0191.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 188 # # ============================================ # Comments from T0191.t2k.alpha.rdb # ============================================ # TARGET T0191 # 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 T0191.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 188 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 I 0.0831 0.0559 0.8610 2 G 0.1309 0.0689 0.8001 3 Y 0.1239 0.1387 0.7373 4 N 0.1070 0.2676 0.6254 5 T 0.0877 0.4190 0.4933 6 D 0.0409 0.7520 0.2071 7 G 0.0121 0.9091 0.0788 8 I 0.0068 0.9470 0.0462 9 G 0.0053 0.9523 0.0424 10 A 0.0044 0.9567 0.0389 11 R 0.0044 0.9564 0.0393 12 M 0.0044 0.9541 0.0415 13 A 0.0044 0.9465 0.0491 14 L 0.0046 0.9404 0.0550 15 E 0.0050 0.9124 0.0826 16 E 0.0079 0.8217 0.1705 17 E 0.0381 0.5421 0.4198 18 I 0.0623 0.1320 0.8057 19 G 0.0927 0.1014 0.8059 20 R 0.1302 0.0860 0.7837 21 V 0.0736 0.2278 0.6986 22 K 0.0308 0.2116 0.7576 23 D 0.0402 0.1103 0.8495 24 K 0.2739 0.0184 0.7077 25 N 0.7920 0.0045 0.2035 26 I 0.9250 0.0042 0.0708 27 V 0.9313 0.0035 0.0651 28 I 0.9245 0.0038 0.0717 29 Y 0.7895 0.0271 0.1834 30 G 0.3637 0.0184 0.6179 31 A 0.0647 0.0995 0.8358 32 G 0.0337 0.3443 0.6219 33 G 0.0065 0.8968 0.0967 34 A 0.0046 0.9439 0.0516 35 A 0.0044 0.9561 0.0396 36 R 0.0044 0.9594 0.0362 37 A 0.0044 0.9593 0.0363 38 V 0.0044 0.9589 0.0368 39 A 0.0044 0.9564 0.0392 40 F 0.0045 0.9515 0.0441 41 E 0.0050 0.9330 0.0620 42 L 0.0067 0.8856 0.1077 43 A 0.0129 0.7603 0.2269 44 K 0.0301 0.4046 0.5652 45 D 0.0340 0.0691 0.8970 46 N 0.1268 0.0160 0.8572 47 N 0.4155 0.0170 0.5676 48 I 0.8820 0.0046 0.1134 49 I 0.9234 0.0037 0.0729 50 I 0.9236 0.0039 0.0726 51 A 0.8470 0.0229 0.1300 52 N 0.6297 0.0086 0.3617 53 R 0.1334 0.0475 0.8191 54 T 0.0934 0.0221 0.8844 55 V 0.0054 0.8536 0.1409 56 E 0.0051 0.9110 0.0839 57 K 0.0047 0.9322 0.0631 58 A 0.0044 0.9504 0.0452 59 E 0.0045 0.9514 0.0441 60 A 0.0044 0.9478 0.0478 61 L 0.0044 0.9455 0.0501 62 A 0.0046 0.9401 0.0553 63 K 0.0051 0.9136 0.0812 64 E 0.0065 0.8626 0.1309 65 I 0.0258 0.7290 0.2453 66 A 0.0193 0.5313 0.4494 67 E 0.0236 0.4697 0.5067 68 K 0.0428 0.3710 0.5862 69 L 0.0627 0.2124 0.7250 70 N 0.0988 0.1851 0.7161 71 K 0.1931 0.2101 0.5968 72 K 0.2485 0.2177 0.5338 73 F 0.3555 0.1674 0.4771 74 G 0.3653 0.0954 0.5393 75 E 0.4879 0.0873 0.4248 76 E 0.5103 0.0810 0.4087 77 V 0.3171 0.0728 0.6102 78 K 0.1579 0.0559 0.7862 79 F 0.0211 0.5995 0.3794 80 S 0.0122 0.6558 0.3320 81 G 0.0138 0.7263 0.2599 82 L 0.0101 0.8038 0.1861 83 D 0.0070 0.8577 0.1354 84 V 0.0071 0.8499 0.1430 85 D 0.0094 0.8034 0.1871 86 L 0.0191 0.7515 0.2293 87 D 0.0149 0.5150 0.4701 88 G 0.0289 0.2446 0.7265 89 V 0.1245 0.0351 0.8405 90 D 0.1374 0.0517 0.8109 91 I 0.9045 0.0050 0.0905 92 I 0.9314 0.0037 0.0649 93 I 0.9270 0.0040 0.0690 94 N 0.8810 0.0070 0.1121 95 A 0.4779 0.0190 0.5031 96 T 0.2080 0.0229 0.7692 97 P 0.1479 0.0571 0.7950 98 I 0.0882 0.1273 0.7846 99 G 0.0689 0.1198 0.8113 100 M 0.0901 0.1104 0.7995 101 Y 0.1196 0.0989 0.7814 102 P 0.1126 0.1309 0.7565 103 N 0.0925 0.1289 0.7786 104 I 0.0605 0.2228 0.7167 105 D 0.0529 0.2119 0.7352 106 V 0.0694 0.2317 0.6989 107 E 0.0946 0.2113 0.6941 108 P 0.1024 0.2173 0.6802 109 I 0.1222 0.2779 0.5999 110 V 0.1085 0.2871 0.6044 111 K 0.0941 0.3176 0.5882 112 A 0.0265 0.7284 0.2451 113 E 0.0281 0.7016 0.2703 114 K 0.0422 0.6210 0.3369 115 L 0.0862 0.3773 0.5365 116 R 0.0790 0.1607 0.7604 117 E 0.0621 0.1134 0.8245 118 D 0.0854 0.0731 0.8415 119 M 0.3991 0.0224 0.5785 120 V 0.8577 0.0052 0.1370 121 V 0.9091 0.0047 0.0862 122 M 0.9026 0.0060 0.0915 123 D 0.8594 0.0106 0.1300 124 L 0.6925 0.0240 0.2835 125 I 0.4842 0.0333 0.4825 126 Y 0.2316 0.0333 0.7351 127 N 0.1101 0.0333 0.8566 128 P 0.0564 0.1310 0.8126 129 L 0.0684 0.1203 0.8113 130 E 0.0516 0.2164 0.7320 131 T 0.0441 0.3617 0.5942 132 V 0.0157 0.8213 0.1630 133 L 0.0105 0.8751 0.1144 134 L 0.0070 0.9211 0.0720 135 K 0.0059 0.9280 0.0661 136 E 0.0050 0.9411 0.0539 137 A 0.0059 0.9365 0.0575 138 K 0.0053 0.9201 0.0746 139 K 0.0066 0.8388 0.1546 140 V 0.0444 0.3497 0.6060 141 N 0.0421 0.0363 0.9216 142 A 0.1790 0.0311 0.7899 143 K 0.6450 0.0356 0.3194 144 T 0.6427 0.0484 0.3089 145 I 0.3782 0.0935 0.5283 146 N 0.1327 0.1275 0.7398 147 G 0.0516 0.3275 0.6208 148 L 0.0303 0.8272 0.1425 149 G 0.0202 0.8880 0.0918 150 M 0.0301 0.9050 0.0649 151 L 0.0586 0.8865 0.0550 152 I 0.0572 0.8906 0.0523 153 Y 0.0397 0.8994 0.0609 154 Q 0.0187 0.8962 0.0851 155 G 0.0130 0.8674 0.1196 156 A 0.0141 0.8368 0.1491 157 V 0.0149 0.7643 0.2208 158 A 0.0186 0.5773 0.4041 159 F 0.0472 0.3214 0.6314 160 K 0.0242 0.0895 0.8863