This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000) in the References section below.
In full display mode, this track displays up to ten different classes of repeats:
The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading.
UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet.
Additionally, the zebunc.ref (Zebrafish Unclassified) library of repeats was added to the zebrafish-specific repeats library used by RepeatMasker. The zebunc.ref set of repeats were obtained from RepBase12.07 from GIRI. Some repeats were removed because the Wellcome Trust Sanger Institute (WTSI) Zebrafish Sequencing Project has determined that these repeats mask out real genes. The following repeats were removed: Dr000898, Dr000899, Dr000900, Dr000972, Dr001021, Dr000650, Dr000651, Dr000652, Dr000848, Dr000849, Dr000850, Dr000851, Dr001204, Dr001205, Dr001206.
Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information.
Thanks to Arian Smit and GIRI for providing the tools and repeat libraries used to generate this track and to the Zebrafish Sequencing Project at WTSI for providing the list of unclassified repeats that mask out genes.
Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2007.
RepBase is described in Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420.
For a discussion of repeats in mammalian genomes, see:
Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6): 657-63.
Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8.