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Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research.
Federico Vello1, Francesco Filippini1, Irene Righetto1
1Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, 35131 Padua, Italy.
Viruses
|September 28, 2024
Summary
Bioinformatics and computational biology tools enhance virus research by leveraging big data from high-throughput sequencing. This article explores valuable information from general and virus-specific databases, including host-pathogen interactions and phylogenetic analysis.
Area of Science:
- Bioinformatics and Computational Biology
- Virology
- Genomics
Background:
- The fields of Bioinformatics and Computational Biology have rapidly advanced, driven by high-throughput sequencing technologies generating vast amounts of biological data.
- The recent SARS-CoV-2 pandemic significantly accelerated the collaboration between bioinformaticians and virologists.
- Viruses, as obligate intracellular parasites, present unique challenges and opportunities for computational analysis.
Purpose of the Study:
- To demonstrate how bioinformatics tools and databases can significantly enhance virus research.
- To highlight the utility of general and virus-specific databases for retrieving critical information on viral sequences and annotations.
- To introduce phylogenetic and phylodynamic tools for analyzing viral evolution and spread.
Main Methods:
- Exploration of general databases within the International Nucleotide Sequence Database Collaboration (INSDC).
- Review of specialized, virus-specific databases and their evolving content.
- Focus on host-pathogen protein-protein interaction databases.
- Illustration of phylogenetic and phylodynamic tools, including algorithms, features, usage, and case studies.
Main Results:
- Significant and useful information regarding viral nucleotide/protein sequences and annotations is accessible through INSDC and dedicated virus databases.
- Host-pathogen interaction databases provide crucial insights into viral mechanisms.
- Phylogenetic and phylodynamic tools effectively analyze viral relationships and population dynamics, validated by practical case studies.
Conclusions:
- Bioinformatics offers powerful resources for advancing virology research.
- Accessible databases and analytical tools are essential for understanding viral biology, evolution, and interactions.
- This work serves as a foundational guide for applying computational approaches in virology.
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