# This file is the result of combining several RDB files, specifically # T0437.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0437.t2k.stride-ebghtl.rdb (weight 1.24869) # T0437.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 T0437.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 51 # # ============================================ # Comments from T0437.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0437 # 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 T0437.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 51 # # ============================================ # Comments from T0437.t2k.str.rdb # ============================================ # TARGET T0437 # 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 T0437.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 51 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0154 0.0249 0.9597 2 K 0.0818 0.1035 0.8147 3 D 0.0835 0.1260 0.7905 4 V 0.0665 0.1621 0.7714 5 V 0.0595 0.1601 0.7804 6 D 0.0572 0.5762 0.3666 7 K 0.0697 0.6007 0.3296 8 C 0.0819 0.6122 0.3059 9 S 0.1063 0.4707 0.4230 10 T 0.1086 0.2872 0.6042 11 K 0.1073 0.1561 0.7366 12 G 0.1200 0.0963 0.7837 13 C 0.2764 0.0880 0.6356 14 A 0.5394 0.0635 0.3972 15 I 0.6481 0.0514 0.3006 16 D 0.7513 0.0272 0.2214 17 I 0.7365 0.0308 0.2327 18 G 0.7683 0.0267 0.2051 19 T 0.8652 0.0180 0.1168 20 V 0.8948 0.0137 0.0915 21 I 0.8869 0.0093 0.1037 22 D 0.5712 0.0181 0.4107 23 N 0.0892 0.0363 0.8745 24 D 0.0492 0.0298 0.9210 25 N 0.1935 0.0229 0.7836 26 C 0.5379 0.0063 0.4557 27 T 0.8895 0.0029 0.1076 28 S 0.9560 0.0025 0.0415 29 K 0.9727 0.0024 0.0249 30 F 0.9663 0.0031 0.0306 31 S 0.9611 0.0028 0.0361 32 R 0.9418 0.0036 0.0546 33 F 0.8424 0.0048 0.1528 34 F 0.5488 0.0133 0.4380 35 A 0.1037 0.0412 0.8551 36 T 0.0356 0.0500 0.9144 37 R 0.0042 0.8851 0.1107 38 E 0.0038 0.9500 0.0462 39 E 0.0038 0.9674 0.0288 40 A 0.0038 0.9722 0.0240 41 E 0.0037 0.9722 0.0241 42 S 0.0037 0.9702 0.0260 43 F 0.0037 0.9677 0.0286 44 M 0.0037 0.9711 0.0252 45 T 0.0037 0.9699 0.0264 46 K 0.0038 0.9589 0.0373 47 L 0.0038 0.9617 0.0345 48 K 0.0037 0.9731 0.0231 49 E 0.0037 0.9675 0.0287 50 L 0.0037 0.9620 0.0342 51 A 0.0037 0.9543 0.0420 52 A 0.0038 0.9425 0.0538 53 A 0.0039 0.9035 0.0926 54 A 0.0055 0.7869 0.2076 55 S 0.0139 0.2734 0.7128 56 S 0.0090 0.2958 0.6952 57 A 0.0100 0.2412 0.7488 58 D 0.0273 0.1474 0.8253 59 E 0.0544 0.0808 0.8648 60 G 0.1342 0.0888 0.7769 61 A 0.3204 0.0886 0.5910 62 S 0.5461 0.0439 0.4100 63 V 0.7031 0.0206 0.2763 64 A 0.7152 0.0153 0.2695 65 Y 0.7492 0.0161 0.2346 66 K 0.8622 0.0107 0.1271 67 I 0.8948 0.0065 0.0988 68 K 0.8612 0.0062 0.1327 69 D 0.8143 0.0130 0.1726 70 L 0.5174 0.0336 0.4491 71 E 0.1866 0.0575 0.7559 72 G 0.0876 0.0392 0.8732 73 Q 0.4181 0.0145 0.5674 74 V 0.8342 0.0031 0.1628 75 E 0.9513 0.0025 0.0462 76 L 0.9459 0.0024 0.0517 77 D 0.9523 0.0024 0.0453 78 A 0.9572 0.0024 0.0403 79 A 0.9589 0.0024 0.0387 80 F 0.9646 0.0024 0.0330 81 T 0.9394 0.0025 0.0581 82 F 0.8936 0.0031 0.1033 83 S 0.8064 0.0094 0.1842 84 C 0.5005 0.0748 0.4246 85 Q 0.3136 0.2306 0.4557 86 A 0.1771 0.6000 0.2230 87 E 0.1030 0.7399 0.1571 88 M 0.1201 0.7865 0.0933 89 I 0.0587 0.8924 0.0489 90 I 0.0151 0.9505 0.0344 91 F 0.0134 0.9434 0.0433 92 E 0.0055 0.9375 0.0570 93 L 0.0084 0.8830 0.1086 94 S 0.0219 0.7656 0.2124 95 L 0.0330 0.6463 0.3207 96 R 0.0298 0.5983 0.3719 97 S 0.0351 0.4624 0.5025 98 L 0.0320 0.2690 0.6989 99 A 0.0119 0.0208 0.9673