ArticleNucleic acids research2012
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers, 1 of them a synthesis that pooled it.
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Who cites it
139 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Meta-Analysis ofG3 (Bethesda, Md.) · 2020Pooled it
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- Transcriptional regulation of the pneumococcal capsule can dictate serotype-specific infection.Nature communications · 2026Article
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- Escherichia coli Type III Secretion System 2 Is Associated With Patient Mortality in Bloodstream Infections.The Journal of infectious diseases · 2025Article
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- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- Aspergillus fumigatus mitogenomes and their influence on azole-resistant and -susceptible populations.npj antimicrobials and resistance · 2025Article
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Using Phylogeny and a Conserved Genomic Neighborhood Analysis to Extract and Visualize Gene Sets Involved in Target Gene Function: The Case of [NiFe]-hydrogenase and Succinate Dehydrogenase.Microbes and environments · 2025Article
- Local emergence and global evolution ofAntimicrobial agents and chemotherapy · 2024Article
- Efficient inference of large prokaryotic pangenomes with PanTA.Genome biology · 2024Article
- Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae.PLoS pathogens · 2024Article
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- A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence.Frontiers in plant science · 2024Article
- High-throughput sequencing explores the genetic variability of endophytic bacteria in three Sichuan bamboo species (Frontiers in microbiology · 2024Article
- Serum susceptibility of Escherichia coli and its association with patient clinical outcomes.PloS one · 2024Article
- Bacteriophage Taxonomy: A Continually Evolving Discipline.Methods in molecular biology (Clifton, N.J.) · 2024Article
79 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Pan-genome ortholog clustering tool (PanOCT) is a tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters where homology-only clustering methods cannot. The results from PanOCT and three commonly used graph-based ortholog-finding programs were compared using a set of four publicly available strains of the same bacterial species. All four methods agreed on ∼70% of the clusters and ∼86% of the proteins. The clusters that did not agree were inspected for evidence of correctness resulting in 85 high-confidence manually curated clusters that were used to compare all four methods.
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