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Sequence Demarcation Tool (SDT), a Free User-Friendly Computer Program Using Pairwise Genetic Identity Calculations
Brejnev Muhizi Muhire1, Philippe Roumagnac2,3, Arvind Varsani4,5
1Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2025
Summary
The Sequence Demarcation Tool (SDT) is a free program for classifying geminivirus sequences. It aids in establishing taxonomic thresholds and classifying new species and genera within the Geminiviridae family.
Area of Science:
- Virology
- Bioinformatics
- Computational Biology
Background:
- Geminiviruses represent a significant genus of plant-pathogenic viruses.
- Accurate classification of geminivirus species is crucial for understanding disease dynamics and developing control strategies.
- Existing methods for whole genome sequence classification can be complex and lack standardization.
Purpose of the Study:
- To introduce the Sequence Demarcation Tool (SDT), a user-friendly program for robust geminivirus classification.
- To highlight SDT's utility in generating pairwise genetic identity calculations for taxonomic purposes.
- To demonstrate SDT's role in establishing demarcation thresholds and classifying new geminivirus taxa.
Main Methods:
- SDT utilizes pairwise genetic identity calculations on unaligned whole genome sequences.
- The program generates publication-quality pairwise identity plots.
- SDT produces color-coded distance matrices for taxonomic classification.
Main Results:
- SDT has been widely adopted by geminivirologists for reproducible sequence classification.
- The tool facilitates the establishment of demarcation thresholds for strains, species, and genera.
- SDT has been instrumental in defining new genera and classifying hundreds of new species within Geminiviridae.
Conclusions:
- SDT provides a robust and reproducible method for classifying geminivirus whole genome sequences.
- The tool supports the application of International Committee on Taxonomy of Viruses (ICTV) demarcation criteria.
- SDT has significantly contributed to the taxonomic advancement of the Geminiviridae family over the past decade.
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