Question: Ucsc Table Track Choice For Transposons
2
gravatar for Bioscientist
9.2 years ago by
Bioscientist1.7k
Bioscientist1.7k wrote:

I'm running some program which requires:

  1. RepeatMasker output, with "satellite" only, and converted to BED file.
  2. Coordinates for transposons(Alu,L1,LTR,SVA,ERV) in BED format.
  3. Coordinates for segmental duplication in BED format.

I'm looking for such output under UCSC/Table Browser/Variation and Repeats group/ There're many lists for the track choice.

I'm quite certain I should choose 'Segmental Dups' track to get duplication output. But for repeatmasker (with satellite only), should I choose "Microsatellite" track? And for transposon, should I choose "Simple Repeats"?

Actually can anyone give explanations about the following track choices:

  • Exapted Repeats
  • RepeatMasker
  • RepMask 3.2.7(difference from RepeatMasker?)
  • Interrupted Rpts
  • Intr Rpts 3.2.7
  • Simple Repeats
  • Microsatellite

Is there any UCSC documentary to explain all these?

thx

repeatmasker ucsc • 8.1k views
ADD COMMENTlink modified 9.2 years ago by Casey Bergman18k • written 9.2 years ago by Bioscientist1.7k
7
gravatar for Casey Bergman
9.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

The key to being able to answer questions like this is to read the details of the track descriptions. I'm assuming you are using hg18, so for each of your queries you can find the answers below.

Concerning your choices: you need to get 1 & 2 by parsing relevant items from the RepeatMasker or RepMask 3.2.7 tables. I would use the RepMask 3.2.7 since this uses a newer version of RepeatMasker. You won't be able to get these directly from the Table Browser but you should be able to filter for what you want easily in Bash/Python/Perl/Galaxy. Also, you should understand that satellite DNA and and microsatellites are not the same things.


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.

ADD COMMENTlink written 9.2 years ago by Casey Bergman18k

thx....this is really good answer...

ADD REPLYlink written 9.1 years ago by Bioscientist1.7k
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