About Repbase Update
Repbase Update (RU) is a database of prototypic sequences representing repetitive DNA from different eukaryotic species. RU is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).
RU has been developed since 1990 under the direction of Jerzy Jurka (the founder), currently at Genetic Information Research Institute.
Most prototypic sequences from RU are consensus sequences of large families and subfamilies of repeats. Smaller families are represented by sequence examples. RU describes many families of repeats unreported anywhere else. Therefore, it was referred to as an "electronic journal." Individual contributions are documented in RU version released in EMBL format. RU is often used in a FASTA format which removes references to the original authors. To remedy the situation, effective September 1 2001 we created a separate electronic journal, Repbase Reports, which publishes all new data to be compiled in RU.
AcknowledgmentsRepbase is currently supported by private funding raised by the Genetic Information Research Institute. Unfortunately, there is little awareness that Repbase is used by RepeatMasker, Censor, REPET etc., and it is not adequately cited. This has a negative impact on public funding. Without such funding, Repbase may become available by subscription only.
Comments and suggestionsIf you have any comments or suggestions about improving Repbase or access to it, feel free to email us.
For more information on Repbase Update see:
- Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research 110:462-467
- Kapitonov, V.V., Pavlicek, A., Jurka, J. Anthology of human repetitive DNA. Encyclopedia of Molecular Cell Biology and Molecular Medicine (Vol. 1, pp. 251-305). Meyers, R.A., ed., Wiley-VCH Verlag GmbH & Co. KGaA Weinheim (2004).
- Jurka, J., Kapitonov, V.V., Smit, A.F.A. Repetitive elements: detection. Nature Encyclopedia of the Human Genome (Cooper, N.D., ed.), vol. 5, pp. 9-14, Nature Publishing Group, London, New York and Tokyo (2003)
- Jurka, J. Repetitive DNA: detection, annotation, and analysis. In Introduction to Bioinformatics: A Theoretical and Practical Approach. (Krawetz, S.A. and Womble D.D., eds), chapter 8, pp. 151-167, Humana Press, Totowa NJ (2003).
- Jurka, J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 9:418-420 (2000)
- Smit AF. (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9:657-663
- Jurka, J. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8:333-337 (1998).
The following table shows the flat-file contents of Repbase Update. Users can also use our online browser interface to extract custom subsets of Repbase Update.
|Name||Type of repeat families||simple.ref||Simple (macrosatellites)||humrep.ref||Human (primate)||humsub.ref||Alu (primate)||rodrep.ref||Rodent|
|cinunc.ref||Ciona intestinalis unclassified|
|invrep.ref||Other Invertebrate (animals)|
|dcotrep.ref||Other Dicot Plants|
|mcotrep.ref||Other Monocot Plants|
|grasrep.ref||Other Grass Plants|
|tmpnemrep.ref||Nematostella vectensis (includes non-annotated TEs)|
|tmplanrep.ref||Branchiostoma floridae (includes non-annotated TEs)|
|tmpxenrep.ref||Xenopus tropicalis (includes non-annotated TEs)|
Subdirectory ./appendix/ contains older versions of sequences that were updated or deleted at some point.