RepeatMasker

RepeatMasker is a tool to detect repeats and low complexity DNA sequences. The RepeatMasker can use nhmmer, cross_match, ABBlast, WUBlast, RMBlast, and Decypher for repeat detection, as well as Dfam and Repbase libraries. The RepeatMasker algorithm outputs annotation and a FASTA file with repeats masked, i.e., replaced by Ns by default.

Topic

Sequence analysis;Sequence composition, complexity and repeats

Detail

  • Operation: Genome annotation

  • Software interface: Command-line user interface

  • Language: Perl, Python

  • License: Open Source License v2.1

  • Cost: Free

  • Version name: 4.1.1

  • Credit: National Human Genome Research Institute (NHGRI)

  • Input: FASTA

  • Output: FASTA, annotation

  • Contact: <a href="http://www.repeatmasker.org/cgi-bin/form2mail?template=feedback.tmpl&title=Feedback%20Form" target="_blank">Online form</a>

  • Collection: -

  • Maturity: Mature

Publications

  • Using RepeatMasker to identify repetitive elements in genomic sequences.
  • Tarailo-Graovac M, Chen N (2009). Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics Chapter 4: Unit 4.10.
  • https://doi.org/10.1002/0471250953.bi0410s25
  • PMID: 19274634
  • PMC: -

Download and documentation

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