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Bioinformatic Approaches for Comparative Analysis of Viruses

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Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2802))

Abstract

The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need adaptations. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. This chapter offers descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. The authors also provide comments and discussion on how viruses’ unique features can affect standard analyses and how to overcome some of the major sources of problems. Protocols and topics emphasize online tools (which are more accessible to users) and give the real experience of what most bioinformaticians do in day-by-day work with command-line pipelines. The topics discussed include (1) clustering related genomes, (2) whole genome multiple sequence alignments for small RNA viruses, (3) protein alignment for marker genes and species affiliation, (4) variant calling and annotation, and (5) virome analyses and pathogen identification.

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Author information

Authors and Affiliations

  1. Hospital Israelita Albert Einstein, Sao Paulo, Brazil

    Erick Gustavo Dorlass & Deyvid Emanuel Amgarten

Authors
  1. Erick Gustavo Dorlass
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  2. Deyvid Emanuel Amgarten
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Editor information

Editors and Affiliations

  1. Department of Biochemistry, University of Sao Paulo, Sao Paulo, SĂŁo Paulo, Brazil

    JoĂŁo Carlos Setubal

  2. Bioinformatics Group, Universität Leipzig, Leipzig, Sachsen, Germany

    Peter F. Stadler

  3. Technische Fakultät, Universität Bielefeld, Bielefeld, Germany

    Jens Stoye

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Dorlass, E.G., Amgarten, D.E. (2024). Bioinformatic Approaches for Comparative Analysis of Viruses. In: Setubal, J.C., Stadler, P.F., Stoye, J. (eds) Comparative Genomics. Methods in Molecular Biology, vol 2802. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3838-5_13

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  • DOI: https://doi.org/10.1007/978-1-0716-3838-5_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3837-8

  • Online ISBN: 978-1-0716-3838-5

  • eBook Packages: Springer Protocols

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