+
+ +
++This track shows the Repeat Masker annotations on the $assemblyDate $em${organism}$noEm/$asmId genome assembly as calculated from a custom library produced by RepeatModeler. +
+ ++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.
+_EOF_ +; + +if ( length($maskingPercent) ) { + printf "Assembly size: %s bases
\n", &AsmHub::commify($asmSize);
+ printf "Sequence masked: %s bases\n", &AsmHub::commify($maskedBases);
+ printf "
+
+_EOF_ +; +print `cat $rmskVersion`; +print <<_EOF_ ++ +_EOF_ +; + +} + +print <<_EOF_ +
+This track employs a technique which chooses the appropriate visual representation for the data based on the +zoom scale, and or the number of annotations currently in view. The track will automatically switch from the +most detailed visualization ('Full' mode) to the denser view ('Pack' mode) when the window size is greater +than 45kb of sequence. It will further switch to the even denser single line view ('Dense' mode) if more than +500 annotations are present in the current view. +
+
+In dense display mode, a single line is displayed denoting the coverage of repeats using a series
+of colored boxes. The boxes are colored based on the classification of the repeat (see below for legend).
+
+
+
+
+
+In pack mode, repeats are represented as sets of joined features. These are color coded as above based on the
+class of the repeat, and the further details such as orientation (denoted by chevrons) and a family label are provided.
+This family label may be optionally turned off in the track configuration.
+
+
+
+
+
+
+The pack display mode may also be configured to resemble the original UCSC repeat track. In this visualization
+repeat features are grouped by classes (see below), and displayed on seperate track lines. 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 the most detailed visualization repeats are displayed as chevron 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 model sequence and provide context for where a repeat fragment originates in its
+consensus or pHMM model. If the length of the unaligned sequence
+is large, an iterruption line and bp size is indicated instead of drawing the extension 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 form the 3' extremity 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 | +
| + | Low_complexity - Low Complexity DNA | +
| + | Satellite - Satellite Repeats | +
| + | RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) | +
| + | 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.
+ ++The RepeatMasker (www.repeatmasker.org) tool was used to generate the datasets found on this track hub. +
+ ++
\n
+Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and +repeat libraries used to generate this track. +
+ ++Smit AFA, Hubley R, Green P. ${em}RepeatMasker Open-3.0${noEm}. + +http://www.repeatmasker.org. 1996-2010. +
+ ++Repbase Update is described in: +
+ ++Jurka J. + +Repbase Update: a database and an electronic journal of repetitive elements. +${em}Trends Genet${noEm}. 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. +${em}Curr Opin Genet Dev${noEm}. 1999 Dec;9(6):657-63. +PMID: 10607616 +
+ ++Smit AF. + +The origin of interspersed repeats in the human genome. +${em}Curr Opin Genet Dev${noEm}. 1996 Dec;6(6):743-8. +PMID: 8994846 +
+_EOF_ + ; +