# This file is the result of combining several RDB files, specifically # T0135.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0135.t2k.stride-ebghtl.rdb (weight 1.24869) # T0135.t2k.str.rdb (weight 1.53983) # T0135.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 T0135.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0135 # 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 T0135.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 14 # # ============================================ # Comments from T0135.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0135 # 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 T0135.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 14 # # ============================================ # Comments from T0135.t2k.str.rdb # ============================================ # TARGET T0135 # 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 T0135.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 14 # # ============================================ # Comments from T0135.t2k.alpha.rdb # ============================================ # TARGET T0135 # 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 T0135.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 14 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0529 0.0427 0.9044 2 A 0.1203 0.0718 0.8079 3 T 0.1026 0.1063 0.7911 4 R 0.0663 0.1403 0.7934 5 T 0.0718 0.1919 0.7363 6 P 0.0598 0.2310 0.7092 7 K 0.1421 0.1985 0.6595 8 L 0.3789 0.1716 0.4495 9 V 0.5423 0.0596 0.3980 10 K 0.7054 0.0482 0.2464 11 H 0.8985 0.0099 0.0916 12 T 0.9105 0.0073 0.0822 13 L 0.9199 0.0076 0.0725 14 L 0.9091 0.0107 0.0802 15 T 0.8656 0.0140 0.1204 16 R 0.7952 0.0147 0.1901 17 F 0.5626 0.0293 0.4081 18 K 0.1932 0.0897 0.7171 19 D 0.0347 0.2245 0.7408 20 E 0.0260 0.1555 0.8185 21 I 0.0765 0.0606 0.8629 22 T 0.0556 0.0540 0.8904 23 R 0.0059 0.8290 0.1650 24 E 0.0049 0.8910 0.1041 25 Q 0.0047 0.9268 0.0685 26 I 0.0044 0.9494 0.0462 27 D 0.0044 0.9548 0.0408 28 N 0.0044 0.9505 0.0451 29 Y 0.0044 0.9481 0.0475 30 I 0.0045 0.9412 0.0543 31 N 0.0048 0.9021 0.0931 32 D 0.0055 0.8636 0.1309 33 Y 0.0063 0.8709 0.1227 34 T 0.0049 0.8748 0.1203 35 N 0.0054 0.8292 0.1654 36 L 0.0075 0.8455 0.1470 37 L 0.0108 0.8095 0.1796 38 D 0.0165 0.6649 0.3186 39 L 0.0384 0.5853 0.3763 40 I 0.1011 0.2489 0.6500 41 P 0.1079 0.2393 0.6528 42 S 0.2351 0.2125 0.5524 43 M 0.6092 0.0845 0.3063 44 K 0.7280 0.0759 0.1961 45 S 0.7843 0.0542 0.1615 46 F 0.7139 0.0515 0.2346 47 N 0.5978 0.0530 0.3492 48 W 0.3383 0.0616 0.6001 49 G 0.1974 0.0610 0.7416 50 T 0.1826 0.0874 0.7300 51 D 0.1929 0.0722 0.7348 52 L 0.1348 0.1267 0.7385 53 G 0.1067 0.1281 0.7652 54 M 0.0659 0.3756 0.5585 55 E 0.0518 0.4080 0.5401 56 S 0.0450 0.4282 0.5268 57 A 0.0317 0.6282 0.3402 58 E 0.0291 0.6709 0.3000 59 L 0.0280 0.6562 0.3158 60 N 0.0418 0.4696 0.4886 61 R 0.0583 0.2133 0.7284 62 G 0.0807 0.0731 0.8462 63 Y 0.1852 0.0270 0.7878 64 T 0.3512 0.0311 0.6177 65 H 0.8530 0.0070 0.1401 66 A 0.9175 0.0039 0.0785 67 F 0.9202 0.0040 0.0758 68 E 0.9003 0.0043 0.0954 69 S 0.7904 0.0090 0.2006 70 T 0.6385 0.0140 0.3474 71 F 0.3517 0.0392 0.6090 72 E 0.1213 0.0638 0.8149 73 S 0.0843 0.0257 0.8899 74 K 0.0077 0.8119 0.1804 75 S 0.0054 0.8743 0.1202 76 G 0.0055 0.9038 0.0907 77 L 0.0046 0.9374 0.0580 78 Q 0.0058 0.9265 0.0677 79 E 0.0052 0.9008 0.0940 80 Y 0.0083 0.8856 0.1061 81 L 0.0110 0.7801 0.2089 82 D 0.0160 0.6150 0.3689 83 S 0.0788 0.1519 0.7693 84 A 0.0083 0.7788 0.2129 85 A 0.0087 0.7900 0.2013 86 L 0.0186 0.8367 0.1447 87 A 0.0696 0.8101 0.1204 88 A 0.1139 0.7404 0.1457 89 F 0.0949 0.7441 0.1610 90 A 0.0649 0.7321 0.2030 91 E 0.0668 0.6584 0.2748 92 G 0.1122 0.6024 0.2853 93 F 0.2114 0.4636 0.3250 94 L 0.1943 0.4402 0.3655 95 P 0.1109 0.5616 0.3275 96 T 0.0771 0.5293 0.3936 97 L 0.1092 0.4602 0.4307 98 S 0.0599 0.3177 0.6224 99 Q 0.0521 0.1844 0.7635 100 R 0.3341 0.0868 0.5791 101 L 0.7548 0.0365 0.2087 102 V 0.8651 0.0229 0.1121 103 I 0.8564 0.0328 0.1108 104 D 0.7610 0.0457 0.1933 105 Y 0.5012 0.1060 0.3927 106 F 0.3822 0.1153 0.5025 107 L 0.2624 0.1023 0.6352 108 Y 0.0530 0.0261 0.9209