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RepeatRunner

RepeatRunner

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.

Topic

Sequence composition, complexity and repeats; DNA

Details

  • 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_ genetics.utah.edu | barry.moore _at_ genetics.utah.edu
  • Collection: -

Publications

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 https://doi.org/10.1016/j.gene.2006.09.011
PMID: 17137733
PMCID: PMC1945102


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