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CiVi: circular genome visualization with unique features to analyze sequence elements.

Lex Overmars1, Sacha A F T van Hijum2, Roland J Siezen3

  • 1CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.

Bioinformatics (Oxford, England)
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Summary

CiVi is a new web tool for creating custom circular maps to analyze microbial genomes. This visualization aids in interpreting genomic elements and experimental data for publication.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Microbial genome analysis requires effective visualization tools.
  • Integrating diverse sequence and quantitative data is challenging.

Purpose of the Study:

  • To develop a user-friendly web-based tool, CiVi, for creating custom circular genome maps.
  • To facilitate the comprehensive analysis and visualization of microbial genomic elements and associated data.

Main Methods:

  • CiVi is a web-based application accessible online.
  • It allows uploading and visualizing various data types including gene names, functional annotations (COG, PFAM), GC content, and subcellular localization.
  • Quantitative data (e.g., expression ratios, read counts) and predicted elements (e.g., regulatory sequences) can be integrated.

Main Results:

  • CiVi enables visualization of genomic elements in the context of genome-wide distribution, experimental data, and local genomic neighborhood.
  • The tool supports the integration of public genome data with custom analysis results.
  • Generated circular maps are suitable for publication.

Conclusions:

  • CiVi provides a versatile platform for microbial genome analysis and data visualization.
  • It empowers both experts and non-experts to interpret complex genomic information effectively.
  • The tool enhances the publication-readiness of genomic analysis results through clear circular mapping.