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Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes
Louis J Taylor1,2, Klaus Strebel3
1Viral Biochemistry Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. louist@upenn.edu.
BMC Microbiology
|January 8, 2017
Summary
Pyviko is a new Python tool that simplifies designing gene knockouts in viruses with overlapping genes. It successfully identified mutations for gene knockouts in over 93% of tested viral gene pairs.
Area of Science:
- Virology
- Molecular Biology
- Bioinformatics
Background:
- Gene knockouts are crucial for studying gene function.
- Designing gene knockouts in viruses is challenging due to overlapping genes.
- Existing software does not address mutations in multiple overlapping amino acid sequences for gene knockouts.
Purpose of the Study:
- To develop a tool for designing gene knockouts in viruses with overlapping genes.
- To simplify experimental design for viral gene knockouts.
Main Methods:
- Developed Pyviko, a Python tool and web interface.
- Tested Pyviko on over 240,000 gene pairs from viral genomes.
Main Results:
- Pyviko successfully identified point mutations for premature stop codons in 93.2% of tested gene-overprinted pairs.
- The tool facilitates molecular cloning and study of viral overprinted genes.
Conclusions:
- Pyviko is an effective tool for designing gene knockouts in complex viral genomes.
- The software simplifies a difficult experimental process for researchers.
