LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Background: Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. Therefore, there is a considerable demand for computational identification of transposable elements. LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs). Results: We have developed a software tool LTRharvest for the de novo detection of full length LTR retrotransposons in large sequence sets. LTRharvest efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of LTRharvest against a gold standard annotation for Saccharomyces cerevisae and Drosophila melanogaster shows a...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: David Ellinghaus, Stefan Kurtz, Ute Willhoeft
• Keywords: Annotation, BMCBI 2008, Software Tool, Transposable Elements