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Comparative Genomics pp 29–53Cite as

Pan-Genome Storage and Analysis Techniques

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity. However, researchers face challenges such as processing and maintaining large datasets while providing accurate and efficient analysis approaches. Comparative genomics methods are required for detecting conserved and unique regions between a set of genomes. This chapter gives an overview of tools available for indexing pan-genomes, identifying the sub-regions of a pan-genome and offering a variety of downstream analysis methods. These tools are categorized into two groups, gene-based and sequence-based, according to the pan-genome identification method. We highlight the differences, advantages, and disadvantages between the tools, and provide information about the general workflow, methodology of pan-genome identification, covered functionalities, usability and availability of the tools.

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Authors and Affiliations

  1. Faculty of Technology, Bielefeld University, Bielefeld, Germany

    Tina Zekic, Guillaume Holley & Jens Stoye

  2. Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Tina Zekic, Guillaume Holley & Jens Stoye

  3. International Research Training Group 1906, Bielefeld University, Bielefeld, Germany

    Tina Zekic, Guillaume Holley & Jens Stoye

Authors
  1. Tina Zekic
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  2. Guillaume Holley
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  3. Jens Stoye
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Correspondence to Jens Stoye .

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Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

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Zekic, T., Holley, G., Stoye, J. (2018). Pan-Genome Storage and Analysis Techniques. In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_2

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