# This file is the result of combining several RDB files, specifically # T0140.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0140.t2k.stride-ebghtl.rdb (weight 1.24869) # T0140.t2k.str.rdb (weight 1.53983) # T0140.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 T0140.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0140 # 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 T0140.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 341 # # ============================================ # Comments from T0140.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0140 # 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 T0140.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 341 # # ============================================ # Comments from T0140.t2k.str.rdb # ============================================ # TARGET T0140 # 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 T0140.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 341 # # ============================================ # Comments from T0140.t2k.alpha.rdb # ============================================ # TARGET T0140 # 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 T0140.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 341 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0633 0.0251 0.9116 2 R 0.2275 0.0587 0.7137 3 G 0.2504 0.0904 0.6592 4 S 0.2489 0.1464 0.6048 5 H 0.3332 0.1627 0.5041 6 H 0.4022 0.1064 0.4913 7 H 0.3608 0.0839 0.5553 8 H 0.2425 0.0388 0.7187 9 H 0.1325 0.0379 0.8296 10 H 0.0705 0.3152 0.6143 11 G 0.1169 0.3485 0.5346 12 S 0.2963 0.2646 0.4391 13 R 0.4429 0.1443 0.4128 14 L 0.4599 0.1234 0.4167 15 Q 0.3518 0.1259 0.5223 16 S 0.2463 0.0806 0.6730 17 G 0.3205 0.0609 0.6186 18 K 0.4820 0.0308 0.4872 19 M 0.6668 0.0168 0.3164 20 T 0.7512 0.0216 0.2273 21 G 0.8624 0.0063 0.1313 22 I 0.9078 0.0044 0.0877 23 V 0.9158 0.0038 0.0804 24 K 0.8864 0.0097 0.1039 25 W 0.8663 0.0098 0.1239 26 F 0.7855 0.0237 0.1908 27 N 0.7646 0.0249 0.2106 28 A 0.5875 0.0841 0.3284 29 D 0.4020 0.1363 0.4617 30 K 0.2565 0.1122 0.6314 31 G 0.2339 0.0579 0.7082 32 F 0.4025 0.0403 0.5572 33 G 0.6857 0.0187 0.2956 34 F 0.8288 0.0103 0.1609 35 I 0.8078 0.0083 0.1839 36 T 0.5618 0.0135 0.4247 37 P 0.0719 0.2888 0.6393 38 D 0.0214 0.2382 0.7404 39 D 0.0563 0.1966 0.7471 40 G 0.0851 0.0972 0.8177 41 S 0.3628 0.0314 0.6058 42 K 0.7785 0.0116 0.2099 43 D 0.8501 0.0106 0.1393 44 V 0.8652 0.0183 0.1165 45 F 0.8613 0.0205 0.1181 46 V 0.8389 0.0339 0.1272 47 H 0.7557 0.0604 0.1839 48 F 0.5985 0.0964 0.3051 49 S 0.4126 0.1467 0.4408 50 A 0.2321 0.1685 0.5995 51 G 0.0967 0.2320 0.6713 52 S 0.0876 0.1936 0.7188 53 S 0.0595 0.4492 0.4913 54 G 0.0333 0.6939 0.2728 55 A 0.0370 0.7588 0.2042 56 A 0.0424 0.7531 0.2044 57 V 0.0605 0.7009 0.2386 58 R 0.0989 0.6487 0.2523 59 G 0.1150 0.5403 0.3447 60 N 0.1828 0.2630 0.5542 61 P 0.1486 0.0772 0.7741 62 Q 0.1011 0.0341 0.8648 63 Q 0.0586 0.0742 0.8672 64 G 0.0645 0.0392 0.8963 65 D 0.4184 0.0115 0.5701 66 R 0.8281 0.0038 0.1682 67 V 0.8854 0.0056 0.1090 68 E 0.8797 0.0052 0.1152 69 G 0.8705 0.0057 0.1238 70 K 0.8916 0.0056 0.1028 71 I 0.9200 0.0032 0.0768 72 K 0.8656 0.0184 0.1160 73 S 0.8984 0.0038 0.0978 74 I 0.8140 0.0079 0.1781 75 T 0.6442 0.0106 0.3452 76 D 0.3935 0.0872 0.5193 77 F 0.2834 0.0465 0.6701 78 G 0.5467 0.0265 0.4268 79 I 0.7935 0.0127 0.1938 80 F 0.9057 0.0050 0.0893 81 I 0.8990 0.0068 0.0942 82 G 0.8925 0.0061 0.1014 83 L 0.6848 0.0233 0.2919 84 D 0.2822 0.0428 0.6750 85 G 0.0566 0.0636 0.8797 86 G 0.0683 0.0425 0.8892 87 I 0.3591 0.0297 0.6112 88 D 0.5022 0.0393 0.4585 89 G 0.7291 0.0302 0.2406 90 L 0.8606 0.0199 0.1195 91 V 0.8467 0.0201 0.1333 92 H 0.7826 0.0271 0.1902 93 L 0.3111 0.3929 0.2959 94 S 0.1491 0.4837 0.3672 95 D 0.1112 0.5964 0.2924 96 I 0.1134 0.5143 0.3723 97 S 0.0992 0.3784 0.5224 98 W 0.0511 0.4192 0.5297 99 A 0.0693 0.4013 0.5294 100 Q 0.1829 0.3236 0.4935 101 A 0.2288 0.2072 0.5640 102 E 0.1285 0.1318 0.7397 103 A 0.0484 0.0510 0.9006