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Comparative Microbial Genome Visualization Using GenomeViz

  • Rohit Ghai
  • Trinad Chakraborty
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

Recent years have brought a tremendous increase in the amount of sequence data from various bacterial genome sequencing projects, an increase that is projected to accelerate over the next years. Comparative genomics of microbial strains has provided us with unprecedented information to describe a bacterial species and examine for microbial diversity. This has allowed us to define core genomes based on genes commonly present in all strains of a species or genus and to identify dispensable regions in the genome harboring genus-, species-, and even strainspecific genes. Nevertheless, the task of organizing and summarizing the data to extract the most informative features remains a challenging yet critical endeavor. Visualization is an effective way of structuring and presenting such information effectively, in a concise and eloquent fashion. The large-scale views unveil commonalities and differences between the genomes that may shed light on their evolutionary relationships and define characteristics that are typical of pathogenicity or other ecological adaptations. We describe GenomeViz, a tool for comparative visualization of bacterial genomes that allows the user to actively create, modify and query a genome plot in a visually compact, user-friendly, and interactive manner.

Key Words

Genome visualization circular genome plots comparative genomics horizontal gene transfer whole genome alignments 

Notes

Acknowledgments

The work reported herein is supported by grants from the Deutsche Forschungsgemeinschaft and the BMBF Network Program Pathogenomics to TC. RG is supported by the Graduate College of Biochemistry of Nucleoprotein Complexes (GK370), Justus Liebig University, Giessen, Germany.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Rohit Ghai
    • 1
  • Trinad Chakraborty
    • 2
  1. 1.Institute of Medical Microbiology, Faculty of MedicineJustus-Liebig UniversityGiessen, GERMANY
  2. 2.Institute of Medical Microbiology, Faculty of MedicineJustus-Liebig UniversityGiessen, GERMANY

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