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Comparative Genomics for Prokaryotes

Protocol
First Online:
Part of the Methods in Molecular Biology book series (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.

Key words

Prokaryotic genome Pangenome analysis Whole genome alignment 
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Notes

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.).

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Department of Biochemistry, Institute of ChemistryUniversity of São PauloSão PauloBrazil
  2. 2.School of ComputingFederal University of Mato Grosso do SulCampo GrandeBrazil
  3. 3.Biocomplexity InstituteVirginia TechBlacksburgUSA

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