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Bioinformatics Shared Resources

Sanford Burnham Prebys Medical Discovery Institute

REPEATMASKER v. 20020713

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.

Where? How?
RepeatMasker is maintained on the emu linux server. 
To run it:  repmask  <dna file>
Last installation and version
The latest installed version is 20020713, installed on October 30, 2002.
Prior installations available

RepeatMasker Homepage.
Free (OSI)
Local contact
IT: Martin Fleming

Technical Data

  • tested on: Linux Debian 3.1
  • emu path: /usr/local/share/RepeatMasker_20020713
  • In default $PATH? no