RepeatMasker Web Server
RepeatMasker screens DNA sequences in FASTA format against the Repbase-derived RepeatMasker library of repetitive elements or against the Dfam database
and returns a masked query sequence ready for database
searches. RepeatMasker also generates a table annotating the masked regions.
Reference: A.F.A. Smit, R. Hubley & P. Green, unpublished data.
Current Version: open-4.0.9 ( Dfam: 3.0 only* )
PLEASE READ FIRST: As of May 20, 2019 GIRI has rescinded our working agreement allowing this service to utilize the RepBase RepeatMasker edition. At this time we can only offer masking using the open database Dfam 3.0, which now includes consensus sequences in addition to profile hidden Markov models for many transposable element families. For the time being users requiring RepBase will need to purchase a commercial or academic license and run RepeatMasker localy. We are working to expand the Dfam database and invite you to visit Dfam ( http://www.dfam.org ) for more information.
Check Current Queue Status
RepeatMasker "open-3.0" is licensed under the Open Source License v2.1.
To obtain a copy of the software to run locally ( on UNIX systems ) go here.
RepeatMasker written and supported by: Arian Smit & Robert Hubley
If you would like to mirror this site please send an email to
the web site manager (firstname.lastname@example.org).
Institute for Systems Biology
This server is made possible by funding from the National Human Genome Research
Institute (NHGRI grant # RO1 HG002939).