<it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons
<p>Abstract</p> <p>Background</p> <p>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 ar...
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| Format: | Article |
| Language: | English |
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BMC
2008-01-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/18 |
| _version_ | 1818530112498302976 |
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| author | Willhoeft Ute Kurtz Stefan Ellinghaus David |
| author_facet | Willhoeft Ute Kurtz Stefan Ellinghaus David |
| author_sort | Willhoeft Ute |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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).</p> <p>Results</p> <p>We have developed a software tool <it>LTRharvest </it>for the <it>de novo </it>detection of full length LTR retrotransposons in large sequence sets. <it>LTRharvest </it>efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of <it>LTRharvest </it>against a gold standard annotation for <it>Saccharomyces cerevisae </it>and <it>Drosophila melanogaster </it>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 <it>LTRharvest </it>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.</p> <p>Conclusion</p> <p><it>LTRharvest </it>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 <it>LTRharvest </it>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.</p> |
| first_indexed | 2024-12-11T17:15:37Z |
| format | Article |
| id | doaj.art-9c800862c79f4539bf2586a624e3fcf9 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T17:15:37Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9c800862c79f4539bf2586a624e3fcf92022-12-22T00:57:22ZengBMCBMC Bioinformatics1471-21052008-01-01911810.1186/1471-2105-9-18<it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposonsWillhoeft UteKurtz StefanEllinghaus David<p>Abstract</p> <p>Background</p> <p>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).</p> <p>Results</p> <p>We have developed a software tool <it>LTRharvest </it>for the <it>de novo </it>detection of full length LTR retrotransposons in large sequence sets. <it>LTRharvest </it>efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of <it>LTRharvest </it>against a gold standard annotation for <it>Saccharomyces cerevisae </it>and <it>Drosophila melanogaster </it>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 <it>LTRharvest </it>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.</p> <p>Conclusion</p> <p><it>LTRharvest </it>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 <it>LTRharvest </it>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.</p>http://www.biomedcentral.com/1471-2105/9/18 |
| spellingShingle | Willhoeft Ute Kurtz Stefan Ellinghaus David <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons BMC Bioinformatics |
| title | <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons |
| title_full | <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons |
| title_fullStr | <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons |
| title_full_unstemmed | <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons |
| title_short | <it>LTRharvest</it>, an efficient and flexible software for <it>de novo </it>detection of LTR retrotransposons |
| title_sort | it ltrharvest it an efficient and flexible software for it de novo it detection of ltr retrotransposons |
| url | http://www.biomedcentral.com/1471-2105/9/18 |
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