# This file is the result of combining several RDB files, specifically # T0356.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0356.t2k.stride-ebghtl.rdb (weight 1.24869) # T0356.t2k.str2.rdb (weight 1.54758) # T0356.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 T0356.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 242 # # ============================================ # Comments from T0356.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 242 # # ============================================ # Comments from T0356.t2k.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 242 # # ============================================ # Comments from T0356.t2k.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 242 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.2921 0.0422 0.6657 2 Y 0.3622 0.0391 0.5987 3 T 0.2255 0.0460 0.7285 4 G 0.1105 0.0373 0.8522 5 R 0.0943 0.0339 0.8718 6 P 0.0797 0.0636 0.8567 7 P 0.0415 0.3252 0.6333 8 D 0.0327 0.4378 0.5295 9 E 0.0475 0.4960 0.4564 10 P 0.0295 0.6251 0.3454 11 A 0.0347 0.6789 0.2864 12 V 0.0395 0.7379 0.2226 13 L 0.0310 0.7307 0.2382 14 G 0.0215 0.7313 0.2472 15 V 0.0143 0.8196 0.1660 16 A 0.0120 0.8354 0.1526 17 L 0.0138 0.8364 0.1498 18 N 0.0141 0.8487 0.1372 19 E 0.0102 0.8830 0.1068 20 V 0.0121 0.8763 0.1116 21 F 0.0097 0.8750 0.1153 22 V 0.0088 0.9179 0.0733 23 P 0.0053 0.9339 0.0608 24 I 0.0051 0.9432 0.0518 25 L 0.0055 0.9316 0.0629 26 Q 0.0055 0.9123 0.0822 27 K 0.0086 0.8418 0.1496 28 Q 0.0215 0.6993 0.2792 29 F 0.0670 0.1959 0.7371 30 P 0.0359 0.1824 0.7817 31 E 0.1235 0.1470 0.7296 32 I 0.5225 0.0634 0.4141 33 V 0.6875 0.0491 0.2634 34 D 0.7905 0.0279 0.1816 35 F 0.7726 0.0274 0.2000 36 Y 0.7315 0.0184 0.2501 37 L 0.5589 0.0142 0.4270 38 P 0.2518 0.0250 0.7232 39 P 0.0598 0.2377 0.7025 40 E 0.0549 0.2197 0.7254 41 G 0.0949 0.2134 0.6918 42 C 0.2195 0.1290 0.6515 43 S 0.4867 0.0717 0.4415 44 Y 0.5509 0.0439 0.4052 45 R 0.6647 0.0265 0.3087 46 L 0.8510 0.0082 0.1408 47 A 0.9116 0.0049 0.0836 48 V 0.9297 0.0030 0.0673 49 V 0.9222 0.0045 0.0733 50 T 0.9115 0.0038 0.0847 51 I 0.8365 0.0185 0.1450 52 K 0.6198 0.0391 0.3412 53 K 0.3722 0.0814 0.5464 54 Q 0.1960 0.0850 0.7190 55 Y 0.0891 0.0456 0.8654 56 A 0.0124 0.4341 0.5535 57 G 0.0115 0.6503 0.3383 58 H 0.0092 0.8610 0.1298 59 A 0.0048 0.9433 0.0519 60 K 0.0047 0.9538 0.0414 61 R 0.0047 0.9553 0.0400 62 V 0.0047 0.9570 0.0383 63 M 0.0047 0.9569 0.0384 64 M 0.0048 0.9549 0.0403 65 G 0.0051 0.9484 0.0466 66 V 0.0054 0.9340 0.0606 67 W 0.0075 0.8628 0.1297 68 S 0.0126 0.6410 0.3464 69 F 0.0241 0.4613 0.5146 70 L 0.0359 0.4047 0.5594 71 R 0.0300 0.3573 0.6127 72 Q 0.0487 0.3577 0.5936 73 F 0.0728 0.2478 0.6794 74 M 0.0998 0.2293 0.6709 75 Y 0.2479 0.1240 0.6280 76 T 0.4510 0.0199 0.5291 77 K 0.6080 0.0398 0.3523 78 F 0.9202 0.0038 0.0760 79 V 0.9303 0.0034 0.0663 80 I 0.9285 0.0034 0.0681 81 V 0.9039 0.0037 0.0923 82 C 0.7319 0.0177 0.2503 83 D 0.2451 0.0335 0.7214 84 D 0.0504 0.1125 0.8371 85 D 0.0931 0.0893 0.8175 86 V 0.1581 0.0682 0.7737 87 N 0.1288 0.0301 0.8411 88 A 0.0294 0.1947 0.7758 89 R 0.0282 0.1289 0.8429 90 D 0.1016 0.0959 0.8025 91 W 0.0055 0.9139 0.0806 92 N 0.0059 0.9353 0.0588 93 D 0.0064 0.9399 0.0538 94 V 0.0064 0.9516 0.0420 95 I 0.0063 0.9516 0.0421 96 W 0.0125 0.9444 0.0432 97 A 0.0135 0.9341 0.0524 98 I 0.0240 0.9069 0.0691 99 T 0.0224 0.8299 0.1477 100 T 0.0373 0.6102 0.3525 101 R 0.0728 0.2442 0.6830 102 M 0.1564 0.0818 0.7618 103 D 0.1255 0.0429 0.8316 104 P 0.0194 0.4167 0.5639 105 A 0.0190 0.3508 0.6301 106 R 0.0713 0.2965 0.6322 107 D 0.2009 0.0781 0.7210 108 T 0.6887 0.0311 0.2802 109 V 0.8567 0.0186 0.1247 110 L 0.8134 0.0263 0.1603 111 V 0.6161 0.0344 0.3495 112 E 0.1679 0.0941 0.7380 113 N 0.0697 0.0466 0.8836 114 T 0.1556 0.0237 0.8207 115 P 0.1795 0.0499 0.7705 116 I 0.2150 0.0613 0.7237 117 D 0.1670 0.0740 0.7589 118 Y 0.1735 0.1315 0.6950 119 L 0.2339 0.1062 0.6599 120 D 0.2180 0.0815 0.7005 121 F 0.1100 0.1786 0.7114 122 A 0.0847 0.1490 0.7663 123 S 0.1081 0.0990 0.7929 124 P 0.1102 0.1120 0.7778 125 V 0.1222 0.1242 0.7536 126 S 0.0771 0.1630 0.7600 127 G 0.0794 0.1333 0.7873 128 L 0.1421 0.1200 0.7379 129 G 0.1856 0.0706 0.7438 130 S 0.3263 0.0404 0.6334 131 K 0.5803 0.0322 0.3875 132 M 0.8651 0.0153 0.1196 133 G 0.8967 0.0116 0.0917 134 L 0.8744 0.0156 0.1100 135 D 0.7956 0.0233 0.1811 136 A 0.5026 0.0773 0.4202 137 T 0.3185 0.0913 0.5901 138 N 0.2364 0.0500 0.7136 139 K 0.1653 0.0709 0.7638 140 W 0.1656 0.0686 0.7657 141 P 0.0841 0.1382 0.7777 142 G 0.0602 0.2247 0.7152 143 E 0.0732 0.2618 0.6650 144 T 0.1048 0.2234 0.6717 145 Q 0.1393 0.1911 0.6696 146 R 0.1998 0.1724 0.6278 147 E 0.2287 0.1745 0.5968 148 W 0.1922 0.1142 0.6936 149 G 0.1425 0.0856 0.7720 150 R 0.1657 0.0911 0.7431 151 P 0.1867 0.0759 0.7374 152 I 0.1888 0.0922 0.7189 153 K 0.1679 0.0562 0.7759 154 K 0.0908 0.0281 0.8811 155 D 0.0598 0.0259 0.9143 156 P 0.0052 0.9179 0.0769 157 D 0.0049 0.9373 0.0578 158 V 0.0049 0.9482 0.0469 159 V 0.0048 0.9555 0.0397 160 A 0.0051 0.9514 0.0436 161 H 0.0050 0.9477 0.0473 162 I 0.0060 0.9466 0.0474 163 D 0.0056 0.9524 0.0420 164 A 0.0052 0.9514 0.0434 165 I 0.0056 0.9449 0.0496 166 W 0.0074 0.9377 0.0549 167 D 0.0069 0.9211 0.0720 168 E 0.0066 0.9006 0.0928 169 L 0.0433 0.5226 0.4342 170 A 0.0518 0.0654 0.8829 171 I 0.0816 0.0365 0.8819 172 F 0.0759 0.1320 0.7921 173 N 0.0645 0.1630 0.7725 174 N 0.0648 0.1404 0.7948 175 G 0.0808 0.0662 0.8530 176 K 0.1299 0.0602 0.8100 177 S 0.0691 0.0446 0.8863