ArticlePLoS computational biology2020
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Genomic determinants of antifungal activity ofFrontiers in microbiology · 2026Article
- On the origins and variation of nucleotide skews of archaeal genomes.Frontiers in microbiology · 2026Article
- Unexplored diversity and molecular genetic signatures of chimallin and phuz encoding phages.BMC genomics · 2025Article
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
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- A novel virus potentially evolved from the N4-like viruses represents a unique viral family:Applied and environmental microbiology · 2024Article
- Nosocomial Transmission of Necrotizing Fasciitis: A Molecular Characterization of Group A Streptococcal DNases in Clinical Virulence.Microorganisms · 2024Article
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- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
- Identification of 1600 replication origins ineLife · 2024Article
- Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution.BMC genomics · 2023Article
- Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep's Milk.International journal of molecular sciences · 2023Article
- Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus.Virus research · 2023Article
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Abstract
GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI's Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.
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