# This file is the result of combining several RDB files, specifically # T0541.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0541.t2k.stride-ebghtl.rdb (weight 1.24869) # T0541.t2k.str.rdb (weight 1.53983) # 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 T0541.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0541 # 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 T0541.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 201 # # ============================================ # Comments from T0541.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0541 # 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 T0541.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 201 # # ============================================ # Comments from T0541.t2k.str.rdb # ============================================ # TARGET T0541 # 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 T0541.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 201 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0162 0.0083 0.9755 2 I 0.0691 0.0218 0.9091 3 P 0.1860 0.0625 0.7515 4 D 0.4474 0.0587 0.4938 5 L 0.7729 0.0317 0.1954 6 V 0.8394 0.0266 0.1340 7 P 0.8355 0.0335 0.1310 8 V 0.7833 0.0367 0.1800 9 S 0.6325 0.0396 0.3279 10 L 0.4458 0.0292 0.5249 11 T 0.2294 0.0229 0.7477 12 P 0.1288 0.1056 0.7656 13 V 0.1130 0.1146 0.7724 14 T 0.1603 0.0728 0.7669 15 V 0.1567 0.0403 0.8030 16 V 0.1620 0.0502 0.7878 17 P 0.0360 0.0479 0.9161 18 N 0.0220 0.0267 0.9513 19 T 0.2092 0.0145 0.7763 20 V 0.5755 0.0045 0.4200 21 N 0.8324 0.0030 0.1646 22 T 0.9252 0.0026 0.0722 23 M 0.9579 0.0024 0.0397 24 T 0.9604 0.0024 0.0372 25 A 0.9734 0.0024 0.0242 26 T 0.9747 0.0024 0.0228 27 I 0.9703 0.0025 0.0272 28 E 0.9257 0.0027 0.0716 29 N 0.7987 0.0044 0.1969 30 Q 0.4344 0.0131 0.5525 31 G 0.3027 0.0212 0.6762 32 N 0.3244 0.0407 0.6349 33 K 0.3018 0.0627 0.6354 34 D 0.2730 0.0627 0.6642 35 S 0.1682 0.0656 0.7662 36 T 0.1264 0.0460 0.8276 37 S 0.2213 0.0296 0.7490 38 F 0.7343 0.0064 0.2593 39 N 0.9241 0.0028 0.0731 40 V 0.9673 0.0025 0.0302 41 S 0.9776 0.0024 0.0200 42 L 0.9754 0.0024 0.0221 43 L 0.9605 0.0028 0.0367 44 V 0.8979 0.0043 0.0978 45 D 0.0758 0.0147 0.9095 46 G 0.0604 0.0176 0.9221 47 I 0.7454 0.0082 0.2465 48 V 0.8852 0.0047 0.1101 49 V 0.8979 0.0043 0.0978 50 D 0.8075 0.0097 0.1828 51 T 0.8108 0.0087 0.1805 52 Q 0.8362 0.0074 0.1564 53 T 0.8215 0.0097 0.1688 54 V 0.6518 0.0382 0.3100 55 T 0.4145 0.0814 0.5041 56 S 0.4392 0.1159 0.4448 57 L 0.4756 0.0550 0.4694 58 E 0.2364 0.0453 0.7183 59 S 0.0504 0.0462 0.9034 60 E 0.0432 0.0268 0.9300 61 N 0.2847 0.0164 0.6989 62 S 0.6733 0.0051 0.3215 63 T 0.8669 0.0032 0.1298 64 N 0.8925 0.0035 0.1040 65 V 0.9225 0.0027 0.0749 66 D 0.9136 0.0026 0.0838 67 F 0.9246 0.0026 0.0728 68 H 0.8767 0.0031 0.1201 69 W 0.8012 0.0056 0.1932 70 T 0.6650 0.0107 0.3243 71 L 0.5468 0.0215 0.4317 72 D 0.4511 0.0368 0.5121 73 G 0.3442 0.0439 0.6120 74 T 0.2584 0.0453 0.6963 75 A 0.1518 0.0492 0.7990 76 N 0.1832 0.0293 0.7874 77 S 0.4471 0.0106 0.5423 78 Y 0.8415 0.0031 0.1554 79 T 0.9476 0.0026 0.0499 80 L 0.9707 0.0024 0.0269 81 T 0.9779 0.0024 0.0197 82 V 0.9775 0.0024 0.0201 83 N 0.9677 0.0025 0.0297 84 V 0.9237 0.0028 0.0735 85 D 0.4052 0.0080 0.5868 86 P 0.0194 0.0249 0.9557 87 E 0.0154 0.0265 0.9581 88 N 0.1267 0.0385 0.8348 89 A 0.4873 0.0294 0.4834 90 V 0.8601 0.0190 0.1209 91 N 0.8899 0.0136 0.0965 92 E 0.8108 0.0210 0.1682 93 G 0.6847 0.0196 0.2957 94 N 0.3680 0.0360 0.5961 95 E 0.1237 0.1154 0.7609 96 S 0.1208 0.0839 0.7953 97 N 0.1726 0.0518 0.7756 98 N 0.3103 0.0284 0.6613 99 T 0.6869 0.0155 0.2976 100 L 0.8245 0.0112 0.1642 101 T 0.8800 0.0087 0.1113 102 A 0.8947 0.0076 0.0977 103 L 0.8861 0.0052 0.1088 104 V 0.7808 0.0060 0.2131 105 G 0.5616 0.0055 0.4329 106 T 0.0454 0.0072 0.9474