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RepeatRunner is a pipeline tool to identify repeated sequences in DNA sequences. The RepeatRunner algorithm uses RepeatMasker to search nucleotide libraries of knowns repeats and BLASTX searches.


Sequence composition, complexity and repeats; DNA


  • Operation: Repeat sequence detection
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: National Human Genomes Research Institute, the Howard Hughes Medical Institute
  • Contact: myandell _at_ | barry.moore _at_
  • Collection: -


Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH "Improved repeat identification and masking in Dipterans." Gene 2007; 389(1):1-9
PMID: 17137733
PMCID: PMC1945102

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