ReviewBioinformatics and biology insights2020
First Steps in the Analysis of Prokaryotic Pan-Genomes.
Review in Bioinformatics and biology insights, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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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.
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Who cites it
65 citing papers in PubMed.
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- Pan-genomic analysis of the multi-drug resistant strains of Mycobacterium tuberculosis.World journal of microbiology & biotechnology · 2026Article
- Systems-level genomic and functional characterization of lipopeptide biosurfactant pathways in Bacillus albus MITWPUB5.World journal of microbiology & biotechnology · 2026Article
- Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.Microbiology spectrum · 2026Article
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- Comparative Genomics ofPathogens (Basel, Switzerland) · 2026Article
- Genomic adaptability and virulence of Bacillus anthracis: a machine learning-based pan-genome and comparative analysis.BMC genomics · 2026Article
- Evolutionary dynamics of type VI secretion systems in fruit fly-associatedFrontiers in microbiology · 2026Article
- Comprehensive Phylogenomic Analyses Support the Reclassification of Multiple Bacteroides Species.Current microbiology · 2025Article
- Phenotypic, secondary metabolite, and genomic characterization of Bacillus siamensis B03 from brackish water with Anti‑Vibrio potential.Archives of microbiology · 2025Article
- Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980).Scientific reports · 2025Article
- Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems.BMC genomics · 2025Article
- Phylogenomic and Pangenomic Assessment of a Mediterranean Strain of Raphidiopsis raciborskii Extends Knowledge of the Global Distribution and Characteristics of a Potentially Toxigenic Cyanobacterium.Environmental microbiology reports · 2025Article
- Identification of Novel Gene-Specific Markers for Differentiating Various PathogenicPathogens (Basel, Switzerland) · 2025Article
- Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.BMC genomics · 2025Article
- Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2025Review
- Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.BMC genomics · 2025Article
- PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.ISME communications · 2025Article
- Beyond H37Rv:Frontiers in microbiology · 2025Review
- From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.BMC genomics · 2024Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.