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Comparative Genomics for Prokaryotes.

João C Setubal1, Nalvo F Almeida2, Alice R Wattam3

  • 1Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil. Setubal@iq.usp.br.

Methods in Molecular Biology (Clifton, N.J.)
|December 27, 2017
PubMed
Summary
This summary is machine-generated.

This chapter reviews genome comparison tools for prokaryotic genomes, focusing on methods using DNA sequences, gene content, or both. These tools aid in studying abundant and accessible prokaryotic genome data.

Keywords:
Pangenome analysisProkaryotic genomeWhole genome alignment

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Prokaryotic genomes (bacteria and archaea) are generally smaller and simpler than eukaryotic genomes.
  • Thousands of prokaryotic genomes have been sequenced, providing abundant data.
  • Prokaryotic gene architecture lacks the complex intron-exon structure found in eukaryotes.

Purpose of the Study:

  • To provide an overview of genome comparison tools.
  • To focus on tools developed for prokaryotic genomes.
  • To cover a range of comparative genomic approaches.

Main Methods:

  • Review of existing genome comparison tools.
  • Categorization of methods based on data type: DNA sequence, gene content, or combined.
  • Discussion of tools applicable to prokaryotic genomics.

Main Results:

  • An overview of various genome comparison methodologies is presented.
  • Tools are discussed based on their reliance on DNA sequence data.
  • Methods utilizing gene content and integrated data types are also covered.

Conclusions:

  • Genome comparison tools are essential for analyzing the vast amount of prokaryotic genomic data.
  • A variety of computational approaches exist for comparing prokaryotic genomes.
  • Understanding these tools facilitates research in prokaryotic genomics.