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

Authors: Hao Wang, Zhao Xu

Addresses: 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

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.

Keywords: LTR retrotransposons; ab initio algorithm; comparative genomics; long terminal repeats; eukaryotic genomes; eukaryotes; genomic sequences; bioinformatics; rice genomes.

DOI: 10.1504/IJBRA.2009.027507

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.4, pp.365 - 377

Published online: 28 Jul 2009 *

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