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Comparative Genomics pp 55–78Cite as

Comparative Genomics for Prokaryotes

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

Abstract

Bacteria and archaea, collectively known as prokaryotes, have in general genomes that are much smaller than those of eukaryotes. As a result, thousands of these genomes have been sequenced. In prokaryotes, gene architecture lacks the intron-exon structure of eukaryotic genes (with an occasional exception). These two facts mean that there is an abundance of data for prokaryotic genomes, and that they are easier to study than the more complex eukaryotic genomes. In this chapter, we provide an overview of genome comparison tools that have been developed primarily (sometimes exclusively) for prokaryotic genomes. We cover methods that use only the DNA sequences, methods that use only the gene content, and methods that use both data types.

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Acknowledgments

This work was supported in part by a CNPq researcher fellowship (J.C.S. and N.F.A.); by CAPES grant 3385/2013 (BIGA project) (J.C.S. and N.F.A.); by Fundect-MS grants TO141/2016 and TO007/2015 (N.F.A); and by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and HumanServices, under contract no. HHSN272201400027C (A.R.W.).

Author information

Authors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil

    João C. Setubal

  2. School of Computing, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil

    Nalvo F. Almeida

  3. Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA

    Alice R. Wattam

Authors
  1. João C. Setubal
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  2. Nalvo F. Almeida
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  3. Alice R. Wattam
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Corresponding author

Correspondence to João C. Setubal .

Editor information

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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Setubal, J.C., Almeida, N.F., Wattam, A.R. (2018). Comparative Genomics for Prokaryotes. 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_3

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7461-0

  • Online ISBN: 978-1-4939-7463-4

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