# This file is the result of combining several RDB files, specifically # T0164.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0164.t2k.stride-ebghtl.rdb (weight 1.24869) # T0164.t2k.str.rdb (weight 1.53983) # T0164.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 T0164.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0164 # 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 T0164.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 195 # # ============================================ # Comments from T0164.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0164 # 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 T0164.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 195 # # ============================================ # Comments from T0164.t2k.str.rdb # ============================================ # TARGET T0164 # 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 T0164.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 195 # # ============================================ # Comments from T0164.t2k.alpha.rdb # ============================================ # TARGET T0164 # 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 T0164.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 195 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.0500 0.0463 0.9037 2 S 0.0454 0.1220 0.8326 3 T 0.0224 0.5534 0.4242 4 D 0.0148 0.7320 0.2532 5 V 0.0075 0.8347 0.1578 6 E 0.0052 0.9133 0.0815 7 E 0.0048 0.9389 0.0562 8 T 0.0045 0.9496 0.0460 9 L 0.0044 0.9531 0.0425 10 K 0.0045 0.9547 0.0408 11 R 0.0046 0.9467 0.0487 12 I 0.0049 0.9334 0.0617 13 Q 0.0073 0.9035 0.0892 14 N 0.0076 0.7412 0.2512 15 N 0.0172 0.4395 0.5433 16 D 0.0774 0.0697 0.8529 17 P 0.0289 0.1442 0.8269 18 D 0.0978 0.1129 0.7893 19 L 0.2913 0.1096 0.5990 20 E 0.5751 0.1222 0.3026 21 E 0.8427 0.0299 0.1274 22 V 0.8376 0.0199 0.1425 23 N 0.7290 0.0206 0.2504 24 L 0.2868 0.1345 0.5787 25 N 0.0591 0.2685 0.6724 26 N 0.0499 0.2503 0.6998 27 I 0.0836 0.2294 0.6870 28 M 0.0876 0.1416 0.7708 29 N 0.0677 0.1226 0.8096 30 I 0.0959 0.0711 0.8329 31 P 0.0615 0.0631 0.8754 32 V 0.0087 0.8453 0.1460 33 P 0.0051 0.9293 0.0656 34 T 0.0046 0.9401 0.0552 35 L 0.0044 0.9567 0.0389 36 K 0.0044 0.9577 0.0379 37 A 0.0044 0.9565 0.0391 38 C 0.0044 0.9549 0.0407 39 A 0.0045 0.9532 0.0423 40 E 0.0046 0.9389 0.0565 41 A 0.0052 0.8989 0.0959 42 L 0.0128 0.8213 0.1659 43 K 0.0124 0.6021 0.3855 44 T 0.0316 0.3196 0.6488 45 N 0.0718 0.0983 0.8299 46 T 0.0469 0.1392 0.8139 47 Y 0.1916 0.0959 0.7124 48 V 0.4852 0.0500 0.4648 49 K 0.6770 0.0680 0.2550 50 K 0.8653 0.0143 0.1203 51 F 0.8402 0.0119 0.1479 52 S 0.7971 0.0115 0.1913 53 I 0.5165 0.0570 0.4265 54 V 0.1880 0.1340 0.6781 55 G 0.0903 0.1268 0.7829 56 T 0.1146 0.0967 0.7886 57 R 0.1207 0.0897 0.7895 58 S 0.1154 0.0833 0.8014 59 N 0.0605 0.0825 0.8571 60 D 0.0153 0.7624 0.2223 61 P 0.0067 0.9219 0.0714 62 V 0.0053 0.9366 0.0582 63 A 0.0044 0.9561 0.0394 64 F 0.0044 0.9589 0.0367 65 A 0.0044 0.9569 0.0387 66 L 0.0044 0.9552 0.0403 67 A 0.0044 0.9549 0.0406 68 E 0.0045 0.9456 0.0498 69 M 0.0051 0.9182 0.0768 70 L 0.0101 0.8784 0.1115 71 K 0.0094 0.7309 0.2597 72 V 0.0167 0.4900 0.4933 73 N 0.0807 0.1154 0.8039 74 N 0.0371 0.1521 0.8107 75 T 0.1431 0.1031 0.7538 76 L 0.4608 0.0469 0.4922 77 K 0.6926 0.0646 0.2428 78 S 0.8828 0.0110 0.1062 79 L 0.8530 0.0091 0.1379 80 N 0.7869 0.0089 0.2041 81 V 0.4756 0.0725 0.4519 82 E 0.1681 0.1485 0.6833 83 S 0.0827 0.1707 0.7466 84 N 0.1006 0.1140 0.7853 85 F 0.1095 0.1155 0.7751 86 I 0.1121 0.1048 0.7831 87 S 0.0582 0.1201 0.8217 88 G 0.0109 0.8086 0.1805 89 S 0.0085 0.9137 0.0778 90 G 0.0050 0.9409 0.0541 91 I 0.0044 0.9585 0.0371 92 L 0.0044 0.9598 0.0359 93 A 0.0044 0.9588 0.0369 94 L 0.0044 0.9576 0.0380 95 V 0.0044 0.9563 0.0392 96 E 0.0046 0.9463 0.0491 97 A 0.0052 0.9100 0.0848 98 L 0.0122 0.8335 0.1543 99 Q 0.0149 0.5953 0.3897 100 S 0.0381 0.2800 0.6819 101 N 0.0702 0.0712 0.8585 102 T 0.0452 0.1433 0.8114 103 S 0.2446 0.1080 0.6475 104 L 0.5608 0.0552 0.3841 105 I 0.7256 0.0688 0.2056 106 E 0.8754 0.0150 0.1096 107 L 0.8256 0.0155 0.1588 108 R 0.7903 0.0151 0.1946 109 I 0.5081 0.0521 0.4398 110 D 0.1878 0.1292 0.6830 111 N 0.0859 0.1262 0.7879 112 Q 0.1099 0.0755 0.8146 113 S 0.0702 0.1264 0.8034 114 Q 0.0667 0.1096 0.8238 115 P 0.0611 0.0933 0.8456 116 L 0.0943 0.0835 0.8222 117 G 0.0620 0.0949 0.8431 118 N 0.0093 0.8301 0.1606 119 N 0.0053 0.9111 0.0837 120 V 0.0052 0.9345 0.0604 121 E 0.0044 0.9544 0.0413 122 M 0.0044 0.9562 0.0394 123 E 0.0044 0.9558 0.0399 124 I 0.0044 0.9565 0.0391 125 A 0.0044 0.9567 0.0389 126 N 0.0045 0.9495 0.0459 127 M 0.0050 0.9333 0.0618 128 L 0.0084 0.9068 0.0848 129 E 0.0083 0.7834 0.2083 130 K 0.0178 0.5021 0.4801 131 N 0.0749 0.1120 0.8132 132 T 0.0385 0.1601 0.8014 133 T 0.1305 0.1432 0.7263 134 L 0.3431 0.1465 0.5105 135 L 0.5214 0.1305 0.3481 136 K 0.7076 0.0749 0.2175 137 F 0.6288 0.0501 0.3211 138 G 0.5314 0.0367 0.4319 139 Y 0.3140 0.0874 0.5986 140 H 0.1616 0.1044 0.7340 141 F 0.1098 0.1296 0.7607 142 T 0.1101 0.1325 0.7574 143 Q 0.1185 0.1177 0.7638 144 Q 0.0853 0.1487 0.7659 145 G 0.0602 0.1377 0.8021 146 P 0.0414 0.4391 0.5195 147 R 0.0316 0.6294 0.3390 148 L 0.0351 0.7123 0.2525 149 R 0.0412 0.7645 0.1943 150 A 0.0274 0.8525 0.1201 151 S 0.0277 0.8482 0.1241 152 N 0.0196 0.8720 0.1084 153 A 0.0220 0.8439 0.1341 154 M 0.0280 0.8052 0.1668 155 M 0.0352 0.7301 0.2346 156 N 0.0412 0.5754 0.3834 157 N 0.0325 0.4952 0.4724 158 N 0.0253 0.5676 0.4071 159 D 0.0254 0.6930 0.2815 160 L 0.0186 0.7995 0.1819 161 V 0.0289 0.8139 0.1572 162 R 0.0338 0.7831 0.1831 163 K 0.0482 0.7351 0.2167 164 R 0.0599 0.6134 0.3267 165 R 0.0597 0.4069 0.5334 166 L 0.0360 0.0594 0.9046