Identification of LTR retrotransposons in eukaryotic genomes: supports from structure and evolution

Authors:
Hao Wang;Zhao Xu
Affiliations:
T-life Research Center, Department of Physics, Fudan University, 220 HanDan Road, Shanghai 200433, China.;T-life Research Center, Department of Physics, Fudan University, 220 HanDan Road, Shanghai 200433, China
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2009

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Abstract

Ubiquitous in eukaryotes, Long Terminal Repeats (LTR) retrotransposons elements play important role in the genome evolution. Sequencing of genomes presents a great challenge of rapidly identifying them in large-scale genomic data. In this report we describe LTR_INSERT, a computational method for identifying LTR elements in genomic sequences. Our method provides structural and evolutionary supports to discover LTR elements. By applying LTR_INSERT to two rice genomes, we have identified 72 novel LTR families in the species of which LTR elements have been extensively mined.