A new repeat-masking method enables specific detection of homologous sequences.
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, TANTAN, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.
Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Sequence Analysis Team, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. martin@cbrc.jp
Martin C
MC
Frith
D020856:AT Rich Sequence; D000465:Algorithms; D004247:DNA / Q000737:chemistry; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
D004247:DNA