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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 sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. This is comparable or slightly better than annotations for previous software tools. The main advantage of  LTRharvest  over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software.    Conclusion   LTRharvest  is an efficient software tool delivering high quality annotation of LTR retrotransposons. It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes  LTRharvest  a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.

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