RepeatMasker Track Settings
 
Repeating Elements by RepeatMasker   (All Annotation tracks)

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Display data as a density graph:

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dense
 Configure 		 SINE  SINE   Schema 
dense
 Configure 		 LINE  LINE   Schema 
dense
 Configure 		 LTR  LTR   Schema 
dense
 Configure 		 DNA  DNA   Schema 
dense
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dense
 Configure 		 Low Complexity  Low Complexity   Schema 
dense
 Configure 		 Satellite  Satellite   Schema 
dense
 Configure 		 RNA  RNA   Schema 
dense
 Configure 		 Other  Other   Schema 
dense
 Configure 		 Unknown  Unknown   Schema 
    

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. RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI).

Display Conventions and Configuration

This track displays ten different classes of repeats:

  • SINE: short interspersed nuclear elements
  • LINE: long interspersed nuclear elements
  • LTR: long terminal repeat elements (including retrotransposons)
  • DNA: DNA repeat elements
  • Simple: simple repeats (microsatellites)
  • Low Complexity: low complexity repeats
  • Satellite: satellite repeats
  • RNA: RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
  • Other: other repeats
  • Unknown: unknown 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.

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

The CB4856 assembly was used as input for RepeatMasker version 4.0.3 (using as its repeat database RepBase update 20140131) specifying "-species elegans" and skipping bacterial insertion element check. We used slow search ("-s") to increase sensitivity, and specificed that the output be in gff format. This output was then converted to bed format for the purpose of browser display.

Credits

Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.

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-4.0. http://www.repeatmasker.org. 2013-2015.

Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1-4):462-7. PMID 16093699