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• Nizhynska, V
• Long, Q
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• Nizhynska, V
• Long, Q

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Biology 2012, 1(2), 395-410; doi:10.3390/biology1020395

Article

TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data

Alexander Platzer, Viktoria Nizhynska and Quan Long*

Gregor Mendel Institute (GMI), Dr. Bohr-Gasse 3, 1030 Vienna, Austria

* Author to whom correspondence should be addressed.

Received: 27 July 2012; in revised form: 22 August 2012 / Accepted: 31 August 2012 / Published: 12 September 2012

(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)

Download PDF Full-Text [936 KB, uploaded 12 September 2012 12:18 CEST]

Abstract: Transposable elements (TEs) are common mobile DNA elements present in nearly all genomes. Since the movement of TEs within a genome can sometimes have phenotypic consequences, an accurate report of TE actions is desirable. To this end, we developed TE-Locate, a computational tool that uses paired-end reads to identify the novel locations of known TEs. TE-Locate can utilize either a database of TE sequences, or annotated TEs within the reference sequence of interest. This makes TE-Locate useful in the search for any mobile sequence, including retrotransposed gene copies. One major concern is to act on the correct hierarchy level, thereby avoiding an incorrect calling of a single insertion as multiple events of TEs with high sequence similarity. We used the (super)family level, but TE-Locate can also use any other level, right down to the individual transposable element. As an example of analysis with TE-Locate, we used the Swedish population in the 1,001 Arabidopsis genomes project, and presented the biological insights gained from the novel TEs, inducing the association between different TE superfamilies. The program is freely available, and the URL is provided in the end of the paper.

Keywords: transposable element; NGS data; calling TEs; paired-end reads; structural variation discovery; GWAS

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