Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes

BMC Microbiology

Software

Klaus Strebel¹  Louis J. Taylor² 

[1] Viral Biochemistry Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA;Viral Biochemistry Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA;Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania Philadelphia, Pennsylvania, USA;

关键词: Virus;    Knockout virus;    Mutation;    Overprinting;    Bioinformatics;    Cloning;    Viral mutant;    Knockout;    Pyviko;   

DOI  :  10.1186/s12866-016-0920-3

 received in 2016-04-27, accepted in 2016-12-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundGene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts.ResultsPyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes.ConclusionsPyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface (http://louiejtaylor.github.io/pyViKO/), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.

【 授权许可】

CC BY   
© The Author(s). 2017