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.

Category

DNA

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

Documentation

RepeatMasker Homepage.

License

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