Tag Archives: transposons

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.

Friday SNPpets

Welcome to our Friday feature link dump: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: TARGeT

target_thumbToday’s tip is on a TARGeT. TARGeT is, as the the paper’s title in the this year’s NAR’s issue states, “a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences.” There are several things you can do at TARGeT. Using BLAST, PHI BLAST, MUSCLE and TreeBest ,the main function of TARGeT is  to quickly obtain gene and transposon families from a query sequence. The tip today is a quick intro to the tool and a search on an R1 non-LTR transposon.

TE insertions in genomes

transposon graphicIn the recent database issue of NAR, there are two reports of transposable element (TE) databases. I already discussed one in an earlier post. That one is a database that includes Gypsy elements (non-LTR retroposons) and retroviruses and aims to be a database “devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements.” Hopefully to develop into a database of all TE’s. The other paper, by Levy et al. (“TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates“)1, I’ll discus briefly here introduces a somewhat different database of transposable elements.

ResearchBlogging.orgAs the paper discusses, TE’s have been implicated in a large number of effects on the vertebrate genome: affecting expression and “contributing to genetic diversity, genomic expansion, genomic content and genomic rearrangements.” Whether these immense changes are the raison d’être for transposable elements or the byproduct of a parasitic DNA element, I’ll leave for discussion (though I would side with the latter), but they are unarguably major factors in genome evolution and don’t fit the definition of “junk DNA.” :D.

Continue reading

Billy Learns about Transposase

A commenter, McBlawg‘s Graham Steel, left a comment about Silobreaker as a possible search engine. Indeed, it is a pretty nice tool. It’s more general news than genomics :), but I did a quick search on “transposon” and found this hilarious, and informative, video clip explaining how transpose rearranges parts of the genome. The video is done in the 50′s “Learning about Sex” style. For your viewing pleasure .

Transposon Database

ResearchBlogging.orgI started my Ph.D. studies into the evolution of non-LTR retrotransposable elements in 1990 and found the world of mobile genetic elements or transposons (aka a long time ago… jumping genes) to be varied, complicated and fascinating. In 1993 I discovered the web. I’ve hoped for and searched for a database of these “Mobile genetic elements [that] are self-contained genomic units capable of proliferating within their host genomes”1 to little satisfaction. Such databases exist such as the Mouse Transposon Insertion Database and the dbRIP (human retrotransposon polymorphisms in humans) and several others. But these almost entirely organism-specific databases. This helps the study of the organism (mobile elements have an effect on the genome), but little in the study of transposons as a class.

So, I was happy to see the latest article in the NAR database issue on GypDB

Continue reading

Non-coding, non-functional or junk ncRNA

ResearchBlogging.orgI just finished reading this paper out this month in PNAS, “Specific expression of long noncoding RNAS.” From the looks of it, the paper has conjured up an interesting discussion in the science blogosphere surrounding the paper and the term “Junk DNA.” Before I get to that discussion, let me give a brief synopsis of and thoughts on the paper (and a link to a ncRNA database at the end). Continue reading