UNIT 4.10 Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

  1. Nansheng Chen

Published Online: 1 MAY 2004

DOI: 10.1002/0471250953.bi0410s05

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Chen, N. 2004. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Current Protocols in Bioinformatics. 5:4.10:4.10.1–4.10.14.

Author Information

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

Publication History

  1. Published Online: 1 MAY 2004
  2. Published Print: MAR 2004

This is not the most recent version of the article. View current version (1 MAR 2009)


The RepeatMasker program is used for identifying repetitive elements in nucleotide sequences for further detailed analyses. Users can run RepeatMasker remotely via a Web site, or, for larger input sequences, the program and its dependent programs may be downloaded and run locally on Unix/Linux computers. The protocols in this chapter detail how to use RepeatMasker both remotely and locally to extract repetitive elements data and mask these repetitive elements in nucleotide sequences.


  • RepeatMasker;
  • cross_match;
  • MaskerAid;
  • Repbase Update;
  • RECON;
  • Repetitive element