ArticleBioinformatics (Oxford, England)2021
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
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- A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression.The EMBO journal · 2026Article
- A Type VII-secreted toxin enables inter-mycobacterial competition.Nature communications · 2026Article
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- Article
- A DNA damage-activated kinase controls bacterial immune pathway expression.bioRxiv : the preprint server for biology · 2026Article
- A phage protein screen identifies triggers of the bacterial innate immune system.Nature microbiology · 2026Article
- A histidine pseudokinase modulates polar growth and cell shape in Streptomyces venezuelae.Communications biology · 2026Article
- Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota.bioRxiv : the preprint server for biology · 2026Article
- A novel reverse lipase toxin substrate of themicroLife · 2026Article
- A small periplasmic protein governs broad physiological adaptations in Vibrio cholerae via regulation of the DbfRS two-component system.Nature communications · 2025Article
- Distinct immunity protein families mediate compartment-specific neutralization of a bacterial toxin.Cell reports · 2025Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryAnalysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run. AVAILABILITY AND IMPLEMENTATION: FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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