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Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case
Alberto Brusati1, Giulia Agostinetto2, Antonia Bruno3
1University of Pavia, Department of Brain and Behavioral Sciences, Pavia, Italy.
Methods in Molecular Biology (Clifton, N.J.)
|December 7, 2023
Summary
The ExTaxsI tool aids in visualizing viral biodiversity from NCBI databases, crucial for post-COVID-19 microbial community analysis. This biological data visualization helps understand viral ecology and pathogenesis, using Monkeypox virus as a case study.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- High-throughput sequencing generates vast biological data, necessitating efficient visualization tools for complex system understanding.
- Post-COVID-19 pandemic, analyzing microbial (viral and bacterial) diversity and interactions is vital for public health interventions.
- Effective visualization of biological data is key to exploring ecological and taxonomic relationships.
Purpose of the Study:
- To demonstrate the ExTaxsI (Exploring Taxonomy Information) tool for retrieving and visualizing viral biodiversity data from NCBI.
- To highlight the tool's capability in generating diverse visualization plots for microbial community exploration.
- To showcase ExTaxsI's utility in understanding viral ecology, evolution, and pathogenesis through interactive data exploration.
Main Methods:
- Utilizing the ExTaxsI tool to access and process viral data from National Center for Biotechnology Information (NCBI) databases.
- Integrating various functions within ExTaxsI to generate multiple types of visualization plots.
- Applying ExTaxsI to the Monkeypox virus as a case study for demonstrating biological data visualization potentials.
Main Results:
- ExTaxsI successfully retrieves viral biodiversity data and generates dynamic, interactive visualization plots.
- The tool facilitates deep dives into ecological and taxonomic relationships among microbial species.
- Case study with Monkeypox virus illustrates insights into viral ecology, evolution, and pathogenesis.
Conclusions:
- ExTaxsI is a valuable tool for biological data visualization, enabling easy, interpretable organization and exploration of microbial biodiversity.
- The tool's interactive features (filters, zoom) enhance dynamic exploration of visualization plots.
- ExTaxsI offers significant perspectives for understanding viral communities and informing public health strategies.
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