The Solution for Repeat-Rich Genomes

Repbase is a comprehensive collection of representative repeat sequences in eukaryotic genomes, and has been an essential genetic sequencing companion since 1992. This unique resource can be utilized either as downloadable software and data files, or as an online resource. Repbase is maintained and managed by the Genetic Information Research Institute (GIRI), a private, non-profit institution devoted to the study and characterization of repetitive or mobile DNA elements in eukaryotic species. Repbase has over 22,000 registered users and the three articles introducing Repbase have been cited by around 3,500 scientific articles.


A large portion of Repbase’s value comes from the downloadable nature of the resource for offline use. This allows for users to carry out complex and numerous analysis over the course of weeks or months after a single download. As a result, online usage data is not representative of the value of the resource. For this reason, Repbase has a flat-rate pricing model, similar to other software tools. The various online tools for Repbase are included in the subscription as well.


DNA in a genome is full of “parasitic repeats” that have randomly accumulated over millennia of evolution. When analyzing genetic sequence data, scientists need a way to keep these repeats from overwhelming their sample data so that they can analyze what is important to them. With its vast collection of curated repeat data for over 100 organisms, Repbase allows researchers to distinguish and mask repetitive sequences from other interesting genomic regions with software such as Censor or RepeatMasker. Even if the genome is newly sequenced, scientists can use Repbase to easily find new repeat families by comparing their data with known repeat sequences available on Repbase.

In addition, because most repetitive sequences within genomes originated from various transposons (transposable elements) as well as integrated viruses, Repbase is fundamental to the studies of transposons and of their impact on genome evolution.

Automated repeat characterization software/system such as RepeatModeler or RECON are valuable tools if using in conjunction with Repbase. Repbase supports masking and characterizing repeats with useful information, which is available only in Repbase such as:

  • Classification of repeat sequences into a particular transposon superfamily
  • Precise transposon boundaries and target site alterations
  • Average identity/similarity of sequence copies to the consensus
  • Reconstructed sequences representing ancestral transposons
  • Protein sequences encoded in transposons

An institutional subscription to Repbase provides unlimited, unrestricted access to online sequence analysis tools (Censor, RTclass1), downloadable software packages (Censor, Repbase Submitter, RTclass1, Alnpack, VisualRepbase, Mase), and Repbase Update data files formatted for use with RepeatMasker, REPET and other tools. These online and downloadable resources provide immense value for researchers studying a wide range of plant, animal, or fungal genomes. Access is enabled for all faculty, staff, and students at your institution, including off-campus access through any proxy IP addresses

Repbase uses RTclass1 for data uploads, a computational tool that assigns an unclassified non-LTR retrotransposon to one of the known clades of non-LTR retrotransposons based on phylogenetic analysis of the reverse transcriptase (RT) domain. This tool is offered as web service as well as downloadable standalone program.

RepbaseSubmitter is a java-based interface for submitting new repeat sequences to Repbase. It eliminates common formatting errors, and automates actions such as calculating sequence lengths, predicting protein coding regions, and positioning the species in proper taxonomic context.

Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. Output includes a map of defragmented repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. It can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Censor is offered as web service as well as downloadable standalone program.

Yes! Off-campus access is possible if you are able to provide us with the IP address(es) for your institution’s proxy server when you subscribe. However, Phoenix Bioinformatics is not able to support Shibboleth or other single-sign-on technologies at this time.

We offer free access to Repbase through online Censor service, which is limited to a few runs per month. If you are a librarian or other individual with purchasing privileges and considering a Repbase subscription for your institution, please contact us and we’d be happy to provide you with a quote.

Many of our subscribers use EZ-Proxy for their off-campus access. If you are a subscriber and need our configuration stanza, it is as follows:

Title Repbase