This track was created 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 a separately curated version of the
Repbase Update repeat library from the
Genetic
Information Research Institute (GIRI).
Repbase Update is described in Jurka (2000) in the References section below.
Alternatively, RepeatMasker can use the new
Dfam database of repeat profile HMMs.
Profile HMMs provide a richer description of the repeat families and when used with
RepeatMasker + nhmmer provide a more
sensitive approach to identifying repeats. Dfam is described in Wheeler et al. (2012)
in the References section below.
Display Conventions and Configuration
In dense display mode, a single line is displayed denoting the coverage of repeats using a series
of black boxes.
In full display mode, the track view is controlled by the scale of the view. At scales between 10 Mb
and 30 kb, this track displays up to ten different classes of repeats (see below) one class per
line. The repeat ranges are denoted as grayscale boxes, reflecting both the size of the repeat and
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.
In full display mode and at scales less than 30 kb, a new detailed display mode is used. Repeats
are displayed as arrow boxes, indicating the size and orientation of the repeat. The interior
grayscale shading represents the divergence of the repeat (see above) while the outline color
represents the class of the repeat. Dotted lines above the repeat and extending left or right
indicate the length of unaligned repeat consensus sequence. If the length of the unaligned sequence
is large, a double interruption line is used to indicate that the unaligned sequence is not to scale.
For example, the following repeat is a SINE element in the forward orientation with average
divergence. Only the 5' proximal fragment of the consensus sequence is aligned to the genome.
The 3' unaligned length (384bp) is not drawn to scale and is instead displayed using a set of
interruption lines along with the length of the unaligned sequence.
Repeats that have been fragmented by insertions or large internal deletions are now represented
by join lines. In the example below, a LINE element is found as two fragments. The solid
connection lines indicate that there are no unaligned consensus bases between the two fragments.
Also note these fragments represent the end of the repeat, as there is no unaligned consensus
sequence following the last fragment.
In cases where there is unaligned consensus sequence between the fragments, the repeat will look like
the following. The dotted line indicates the length of the unaligned sequence between the two
fragments. In this case the unaligned consensus is longer than the actual genomic distance between
these two fragments.
If there is consensus overlap between the two fragments, the joining lines will be drawn to indicate
how much of the left fragment is repeated in the right fragment.
The following table lists the repeat class colors:
Color
Repeat Class
SINE - Short Interspersed Nuclear Element
LINE - Long Interspersed Nuclear Element
LTR - Long Terminal Repeat
DNA - DNA Transposon
Simple - Single Nucleotide Stretches and Tandem Repeats
Other - Other Repeats (including class RC - Rolling Circle)
Unknown - Unknown Classification
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
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.
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.