Description
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 Update library of repeats from the
Genetic
Information Research Institute (GIRI).
Repbase Update is described in Jurka (2000) in the References section below.
Some newer assemblies have been made with Dfam, not Repbase. You can
find the details for how we make our database data here in our "makeDb/doc/"
directory.
When analyzing the data tables of this track, keep in mind that Repbase is not the same
as the Repeatmasker sequence database and that the repeat names in the
Repeatmasker output are not the same as the sequence names in the Repeatmasker
database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker
output and this track, but there is not necessarily a single sequence "L1PA4"
in the Repeatmasker database. This is because Repeatmasker creates annotations
by joining matches to partial pieces of the database together so there is no
1:1 relationship between its sequence database and the annotations. To learn
more, you can read the Repeatmasker paper, its source code or reach out to the
Repeatmasker authors, your local expert on transposable elements or us.
Display Conventions and Configuration
In full display mode, this track displays up to ten different classes of repeats:
- Short interspersed nuclear elements (SINE), which include ALUs
- Long interspersed nuclear elements (LINE)
- Long terminal repeat elements (LTR), which include retroposons
- DNA repeat elements (DNA)
- Simple repeats (micro-satellites)
- Low complexity repeats
- Satellite repeats
- RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
- Other repeats, which includes class RC (Rolling Circle)
- Unknown
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.
A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that
the curator was unsure of the classification. At some point in the future,
either the "?" will be removed or the classification will be changed.
Methods
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.
Credits
Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and
repeat libraries used to generate this track.
References
Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0.
https://www.repeatmasker.org/. 1996-2010.
Repbase Update is described in:
Jurka J.
Repbase Update: a database and an electronic journal of repetitive elements.
Trends Genet. 2000 Sep;16(9):418-420.
PMID: 10973072
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.
PMID: 10607616
Smit AF.
The origin of interspersed repeats in the human genome.
Curr Opin Genet Dev. 1996 Dec;6(6):743-8.
PMID: 8994846