ArticleCurrent genomics2015
Inside the Pan-genome - Methods and Software Overview.
Article in Current genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
52 citing papers in PubMed.
- Comparative pathogenomics and in silico analysis of energy metabolism in Acinetobacter baumannii ST195 and novel Turkish isolates encoding blaOXA-23, blaOXA-66, and blaOXA-852.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Pangenomic and genomic plasticity analyses of the genus Rickettsia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- The pangenome: a statistical model, not a fixed biological property.Bioinformatics advances · 2026Review
- Identification of virulence genes and clade-specific markers through pan-genomic analysis of Leptospira.BMC microbiology · 2025Article
- Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2025Review
- PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.ISME communications · 2025Article
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Pangenome Analysis Reveals Novel Contact-Dependent Growth Inhibition System and Phenazine Biosynthesis Operons inMicroorganisms · 2024Article
- Clinical manifestations, antimicrobial resistance and genomic feature analysis of multidrug-resistant Elizabethkingia strains.Annals of clinical microbiology and antimicrobials · 2024Article
- Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove forAntibiotics (Basel, Switzerland) · 2024Review
- Genome and pan-genome analysis of a new exopolysaccharide-producing bacteriumFrontiers in microbiology · 2024Article
- Screening Marine Microbial Metabolites as Promising Inhibitors ofBioMed research international · 2024Article
- Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes.PloS one · 2024Article
- Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness.Microbiology spectrum · 2023Article
- Comparative Genomics ofAntibiotics (Basel, Switzerland) · 2023Article
- Article
- Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS.Plants (Basel, Switzerland) · 2022Review
- Pathogenome comparison and global phylogeny of Escherichia coli ST1485 strains.Scientific reports · 2022Article
- Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be "open" as long as new genes are added significantly to the total repertoire for each new additional genome and "closed" when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.
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Registered trials
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