What’s the Answer? Repeats & Transposable elements in UCSC Genome Browser

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is….

UCSC Table Track choice for transposons

The answer is an excellent rundown of the tracks available in the UCSC genome and table browsers for transposons, repeats and the like:

Exapted Repeats: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=exaptedRepeats

This track displays conserved non-exonic elements that have been deposited by mobile elements (repeats), a process termed “exaptation” (Gould et al., 1982). These regions were identified during a genome-wide survey (Lowe et al., 2007) with the expectation that regions of this type may act as distal transcriptional regulators for nearby genes. A previous case study experimentally verified an exapted mobile element acting as a distal enhancer (Bejerano et al. , 2006).

RepeatMasker: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=rmsk

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).

RepMask 3.2.7: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=rmskRM327

This track was created by using a more recent version (3.2.7, Jan. 2009) of 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, as well as a modified version of the query sequence in which all the annotated repeats have been masked.

Interrupted Rpts: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=nestedRepeats

This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000) in the References section below. The detailed annotations from RepeatMasker are in the RepeatMasker track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output.

Intr Rpts 3.2.7: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=nestedRepeatsRM327

This track shows joined fragments of interrupted repeats extracted from the output of a more recent version (3.2.7, Jan. 2009) of the RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000) in the References section below. The detailed annotations from RepeatMasker are in the RepMask 3.2.7 track. This track shows fragments of original repeat insertions which have been interrupted by insertions of younger repeats or through local rearrangements. The fragments are joined using the ID column of RepeatMasker output. Interrupted repeats from the original RepeatMasker run have been kept in the Interrupted Rpts track in order to avoid disrupting any analyses performed on the original run’s results.

Simple Repeats: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=simpleRepeat

This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF), which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases.

Microsatellite: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=215014537&c=chrX&g=microsat

This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats, and tend to be highly polymorphic in the population.