A new repeat-masking method enables specific detection of homologous sequences

Nucleic Acids Res. 2011 Mar;39(4):e23. doi: 10.1093/nar/gkq1212. Epub 2010 Nov 24.


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.

Publication types

  • Evaluation Study

MeSH terms

  • AT Rich Sequence
  • Algorithms
  • DNA / chemistry
  • Repetitive Sequences, Nucleic Acid
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Sequence Homology, Amino Acid*
  • Sequence Homology, Nucleic Acid*


  • DNA