# This file is the result of combining several RDB files, specifically # T0453.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0453.t2k.stride-ebghtl.rdb (weight 1.24869) # T0453.t2k.str2.rdb (weight 1.54758) # T0453.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 T0453.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0453 # 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 T0453.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 825 # # ============================================ # Comments from T0453.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0453 # 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 T0453.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 825 # # ============================================ # Comments from T0453.t2k.str2.rdb # ============================================ # TARGET T0453 # 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 T0453.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 825 # # ============================================ # Comments from T0453.t2k.alpha.rdb # ============================================ # TARGET T0453 # 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 T0453.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 825 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0796 0.0780 0.8425 2 G 0.0410 0.3399 0.6190 3 E 0.0570 0.3025 0.6405 4 E 0.1024 0.2646 0.6330 5 D 0.1844 0.2299 0.5857 6 E 0.3392 0.2218 0.4390 7 I 0.6234 0.1096 0.2670 8 V 0.7308 0.0690 0.2001 9 Q 0.7802 0.0451 0.1746 10 R 0.5222 0.0683 0.4095 11 E 0.2249 0.0660 0.7091 12 D 0.0466 0.0342 0.9192 13 G 0.0735 0.0355 0.8910 14 S 0.6989 0.0090 0.2921 15 W 0.9102 0.0036 0.0862 16 L 0.9116 0.0049 0.0836 17 V 0.8769 0.0112 0.1119 18 D 0.7014 0.0315 0.2671 19 G 0.5460 0.0301 0.4239 20 M 0.5718 0.0244 0.4038 21 V 0.6262 0.0077 0.3661 22 S 0.4303 0.0097 0.5600 23 L 0.0078 0.8940 0.0981 24 D 0.0049 0.9384 0.0567 25 R 0.0050 0.9465 0.0484 26 F 0.0048 0.9517 0.0435 27 R 0.0051 0.9467 0.0482 28 E 0.0058 0.9290 0.0652 29 F 0.0080 0.8963 0.0957 30 F 0.0530 0.5650 0.3821 31 E 0.0487 0.0861 0.8652 32 L 0.0902 0.0494 0.8604 33 E 0.1519 0.0619 0.7862 34 A 0.1294 0.0989 0.7717 35 P 0.0894 0.1263 0.7843 36 L 0.0811 0.1162 0.8027 37 P 0.0797 0.1690 0.7512 38 G 0.0607 0.1927 0.7466 39 E 0.0488 0.3263 0.6248 40 A 0.0426 0.3765 0.5809 41 G 0.0476 0.3818 0.5706 42 G 0.0579 0.2881 0.6540 43 N 0.0766 0.2581 0.6653 44 I 0.1240 0.2750 0.6011 45 H 0.1727 0.3460 0.4812 46 T 0.1972 0.5309 0.2719 47 L 0.0678 0.8241 0.1081 48 A 0.0238 0.9148 0.0614 49 G 0.0186 0.9305 0.0509 50 V 0.0261 0.9318 0.0421 51 M 0.0393 0.9226 0.0381 52 L 0.0396 0.9164 0.0440 53 Y 0.0232 0.9090 0.0678 54 Q 0.0235 0.8648 0.1117 55 L 0.0505 0.4626 0.4869 56 G 0.0400 0.0607 0.8993 57 R 0.1123 0.0402 0.8475 58 V 0.3810 0.0247 0.5943 59 P 0.1513 0.0257 0.8230 60 S 0.1165 0.0379 0.8456 61 V 0.0656 0.0767 0.8577 62 T 0.0606 0.0442 0.8952 63 D 0.3411 0.0187 0.6401 64 R 0.8196 0.0058 0.1746 65 F 0.8908 0.0050 0.1043 66 E 0.8858 0.0047 0.1095 67 W 0.7436 0.0189 0.2375 68 N 0.1291 0.0484 0.8225 69 G 0.0825 0.0471 0.8704 70 F 0.7358 0.0052 0.2591 71 S 0.9111 0.0040 0.0850 72 F 0.9249 0.0036 0.0715 73 E 0.9190 0.0041 0.0769 74 V 0.9166 0.0029 0.0805 75 V 0.8600 0.0187 0.1213 76 D 0.8347 0.0054 0.1599 77 M 0.5219 0.0408 0.4373 78 D 0.1955 0.0449 0.7596 79 R 0.0935 0.0794 0.8271 80 T 0.3057 0.0549 0.6394 81 R 0.7931 0.0111 0.1958 82 V 0.8484 0.0036 0.1481 83 D 0.8395 0.0198 0.1408 84 K 0.9150 0.0035 0.0815 85 I 0.9109 0.0048 0.0843 86 L 0.9178 0.0037 0.0785 87 V 0.8682 0.0052 0.1266 88 Q 0.5722 0.0147 0.4131 89 R 0.2670 0.0376 0.6954 90 H 0.0771 0.0524 0.8705 91 H 0.0479 0.0359 0.9162