# This file is the result of combining several RDB files, specifically # T0243.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0243.t2k.stride-ebghtl.rdb (weight 1.24869) # T0243.t2k.str2.rdb (weight 1.54758) # T0243.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 T0243.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t2k.str2.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t2k.alpha.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0688 0.0728 0.8584 2 K 0.1532 0.1755 0.6714 3 I 0.1375 0.3705 0.4920 4 R 0.1353 0.4409 0.4238 5 K 0.1469 0.5059 0.3472 6 Y 0.1844 0.4896 0.3261 7 M 0.2433 0.4321 0.3245 8 R 0.3116 0.3943 0.2941 9 I 0.2937 0.4380 0.2684 10 N 0.3332 0.3737 0.2931 11 Y 0.3853 0.4338 0.1809 12 Y 0.5755 0.2913 0.1332 13 I 0.7124 0.1813 0.1064 14 I 0.7849 0.1146 0.1005 15 L 0.7582 0.1209 0.1209 16 K 0.7584 0.1197 0.1219 17 V 0.8018 0.0914 0.1068 18 L 0.8225 0.0715 0.1060 19 V 0.7909 0.0766 0.1325 20 I 0.6224 0.0985 0.2790 21 N 0.2449 0.0952 0.6599 22 G 0.0666 0.1867 0.7467 23 S 0.0891 0.3508 0.5600 24 R 0.0879 0.5073 0.4048 25 L 0.0620 0.5740 0.3641 26 E 0.0570 0.5664 0.3766 27 K 0.0483 0.6458 0.3059 28 K 0.0560 0.6344 0.3097 29 R 0.0585 0.6570 0.2845 30 L 0.0670 0.6450 0.2880 31 R 0.0434 0.7328 0.2238 32 S 0.0309 0.8006 0.1685 33 E 0.0304 0.8033 0.1663 34 I 0.0386 0.7966 0.1648 35 L 0.0522 0.7371 0.2107 36 K 0.0675 0.6481 0.2844 37 R 0.1015 0.5062 0.3924 38 F 0.1942 0.2703 0.5355 39 D 0.2725 0.1190 0.6086 40 I 0.3477 0.1256 0.5267 41 D 0.3165 0.0953 0.5882 42 I 0.1815 0.2186 0.5999 43 S 0.1218 0.2140 0.6643 44 D 0.0663 0.2059 0.7279 45 G 0.0795 0.1776 0.7429 46 V 0.3473 0.2055 0.4472 47 L 0.4292 0.2686 0.3021 48 Y 0.3169 0.3841 0.2990 49 P 0.1751 0.5889 0.2360 50 L 0.1027 0.6749 0.2224 51 I 0.0864 0.7159 0.1977 52 D 0.0612 0.7344 0.2044 53 S 0.0519 0.7219 0.2262 54 L 0.0592 0.6759 0.2649 55 I 0.0643 0.6154 0.3203 56 D 0.0528 0.5470 0.4002 57 D 0.0420 0.5789 0.3790 58 K 0.0653 0.5975 0.3372 59 I 0.1284 0.5497 0.3219 60 L 0.1530 0.4636 0.3834 61 R 0.1472 0.4297 0.4231 62 E 0.1216 0.4513 0.4271 63 E 0.1312 0.3724 0.4964 64 E 0.1681 0.2531 0.5789 65 A 0.1110 0.1210 0.7680 66 P 0.0553 0.1448 0.8000 67 D 0.0621 0.0822 0.8557 68 G 0.1030 0.0565 0.8406 69 K 0.3292 0.0360 0.6348 70 V 0.7877 0.0156 0.1967 71 L 0.8225 0.0262 0.1513 72 F 0.8391 0.0206 0.1403 73 L 0.7432 0.0384 0.2184 74 T 0.4517 0.0767 0.4716 75 E 0.1999 0.2655 0.5346 76 K 0.0730 0.2800 0.6470 77 G 0.0621 0.2935 0.6443 78 M 0.0639 0.4646 0.4714 79 K 0.0629 0.6190 0.3181 80 E 0.0403 0.6946 0.2651 81 F 0.0235 0.8102 0.1663 82 E 0.0174 0.8480 0.1346 83 E 0.0142 0.8657 0.1201 84 L 0.0094 0.8886 0.1021 85 H 0.0110 0.8894 0.0996 86 E 0.0087 0.8860 0.1053 87 F 0.0100 0.8778 0.1122 88 F 0.0246 0.8214 0.1540 89 K 0.0251 0.7564 0.2185 90 K 0.0441 0.6860 0.2699 91 I 0.0949 0.4912 0.4140 92 V 0.1142 0.1976 0.6881 93 C 0.0495 0.0334 0.9171