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Updated: Apr 23, 2026

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

Brejnev Muhizi Muhire¹, Arvind Varsani², Darren Patrick Martin¹

¹Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa.

|September 27, 2014

Summary

This summary is machine-generated.

A new computer program, Sequence Demarcation Tool (SDT), offers objective and reproducible viral genome classification using pairwise genetic identity. This tool addresses inconsistencies in current methods, aiding taxonomic classification.

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Area of Science:

Virology
Bioinformatics
Computational Biology

Background:

The rapid increase in viral genome sequencing necessitates automated, objective classification tools.
Current taxonomic classification relies on pairwise genetic identity but faces challenges with accuracy and consistency.
Issues include score deflation in large datasets and inconsistencies due to handling of alignment gap-characters.

Purpose of the Study:

To introduce Sequence Demarcation Tool (SDT), a user-friendly program for robust and reproducible viral genome classification.
To provide a reliable method for objective classification based on pairwise genetic identity calculations.
To support the International Committee on Taxonomy of Viruses (ICTV) in applying taxonomic demarcation criteria.

Main Methods:

Development of Sequence Demarcation Tool (SDT), a computational program for sequence analysis.
Utilizes pairwise genetic identity calculations for classifying nucleotide and amino acid sequences.
Incorporates features for generating publication-quality identity plots and distance matrices.

Main Results:

SDT offers a robust and reproducible approach to viral genome classification.
The program addresses and mitigates inconsistencies arising from alignment gap-character handling.
Provides visualization tools to aid in sequence classification according to ICTV criteria.

Conclusions:

SDT provides a valuable computational solution for the objective classification of viral genomes.
The tool enhances the accuracy and consistency of taxonomic assignments in virology.
Available in graphical and command-line versions for diverse user needs and platforms.