TEclass—a tool for automated classification of unknown eukaryotic transposable elements

Abrusán, György; Grundmann, Norbert; DeMester, Luc; Makałowski, Wojciech

doi:10.1093/bioinformatics/btp084

Cited by 299 publications

(221 citation statements)

References 5 publications

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“…However, unlike tools like TEclass [54], which makes use of the profiles of frequent k -mers from the Repbase Update databank, our TE classifier guides output classification by detailing the precise TE features present on the analyzed sequences, such as terminal repeats and matches with known TEs. Our tool and REPclass [55] are very similar, but our TE classifier has several advantages.…”

Section: Discussionmentioning

confidence: 99%

Considering Transposable Element Diversification in De Novo Annotation Approaches

Flutre

Duprat²,

Feuillet³

et al. 2011

PLoS ONE

468

455

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Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.

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Section: Discussionmentioning

confidence: 99%

Considering Transposable Element Diversification in De Novo Annotation Approaches

Flutre

Duprat²,

Feuillet³

et al. 2011

PLoS ONE

468

455

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show abstract

“…Low-complexity repeats and tandem repeats were removed as part of the RepeatScout algorithm, using Nseg (Wootton and Federhen, 1993) and Tandem Repeat Finder (Benson, 1999). TEclass, a tool for automated classification of unknown eukaryotic TEs (Abrusán et al, 2009), was run using a 2010/01/20 version of RepBase. The larger value was reported when RepeatMasker and TEclass predicted different counts for certain TE classes.…”

Section: Repeat Contentmentioning

confidence: 99%

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

et al. 2012

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Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maizeinfecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.

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“…Likewise, some programs specifically target the identification of tandem repeated features (e.g., microsatellites and minisatellites) [23,24]. When TE sequences have been identified and/or consensus sequences have been built, these libraries can be classified with devoted programs [25][26][27] and used as probes for sensitive alignment-based genome annotation using popular programs such as RepeatMasker [28] and Censor [29] or combiners such as TEannot from the REPET package [30].…”

Section: Te Proportion Explains Genome Size Variation In Insectsmentioning

confidence: 99%

Impact of transposable elements on insect genomes and biology

Maumus¹,

Fiston-Lavier

Quesneville³

2015

Current Opinion in Insect Science

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TEclass—a tool for automated classification of unknown eukaryotic transposable elements

Abstract: http://www.compgen.uni-muenster.de/teclass, stand alone program upon request.

Cited by 299 publications

References 5 publications

Considering Transposable Element Diversification in De Novo Annotation Approaches

Considering Transposable Element Diversification in De Novo Annotation Approaches

Genome Comparison of Barley and Maize Smut Fungi Reveals Targeted Loss of RNA Silencing Components and Species-Specific Presence of Transposable Elements

Impact of transposable elements on insect genomes and biology

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