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Finding and Characterizing Repeats in Plant Genomes

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Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1374))

Abstract

Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of available software that can help biologists to look for these repeats and check some hypothetical models intended to characterize their structures. Since transposable elements are a major source of repeats in plants, many methods have been used or developed for this large class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided a whole section on this topic as well as a selection of the main existing software. In order to better understand how they work and how repeats may be efficiently found in genomes, it is necessary to look at the technical issues involved in the large-scale search of these structures. Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns. The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences. This can be seen as the first stage of a very general approach called linguistic analysis that is interested in the analysis of natural or artificial texts. Words, the lexical level, correspond to simple repeated entities in texts or strings. In fact, biologists need to represent more complex entities where a repeat family is built on more abstract structures, including direct or inverted small repeats, motifs, composition constraints as well as ordering and distance constraints between these elementary blocks. In terms of linguistics, this corresponds to the syntactic level of a language. The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis.

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Notes

  1. 1.

    http://bergmanlab.smith.man.ac.uk/?page_id=295

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Authors and Affiliations

  1. Dyliss Team, Irisa/Inria Centre de Rennes Bretagne Atlantique, Campus de Beaulieu, 35510, Rennes cedex, France

    Jacques Nicolas

  2. Irisa/Inria Centre de Rennes Bretagne Atlantique, Campus de Beaulieu, 35510, Rennes cedex, France

    Pierre Peterlongo

  3. LCB, CNRS UMR 7283, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France

    Sébastien Tempel

Authors
  1. Jacques Nicolas
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  2. Pierre Peterlongo
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  3. Sébastien Tempel
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Corresponding author

Correspondence to Jacques Nicolas .

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Editors and Affiliations

  1. School of Plant Biology, University of Western Australia, Perth, Australia

    David Edwards

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Nicolas, J., Peterlongo, P., Tempel, S. (2016). Finding and Characterizing Repeats in Plant Genomes. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_17

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  • DOI: https://doi.org/10.1007/978-1-4939-3167-5_17

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

  • eBook Packages: Springer Protocols

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