ArticleBioinformatics (Oxford, England)2012
PGAP: pan-genomes analysis pipeline.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 323 papers, 1 of them a synthesis that pooled it.
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Who cites it
323 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic strategies for sex-biased persistence of gut microbes across human life.Nature communications · 2023Pooled it
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- Draft genome sequence of aMicrobiology resource announcements · 2026Article
- Genome-wide characterization and comparative analysis of Bacillus paranthracis MBBL1 reveals genomic plasticity features.Functional & integrative genomics · 2026Article
- Draft genome sequences ofMicrobiology resource announcements · 2026Article
- Draft genome sequences ofMicrobiology resource announcements · 2026Article
- Genome sequences ofMicrobiology resource announcements · 2026Article
- ARKbase: Antimicrobial Resistance Knowledgebase1.0.Nucleic acids research · 2026Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Genome-based classification of Halonovum salinarum gen. nov., sp. nov., and Halonovum rutilum sp. nov., two novel halophilic archaea isolated from a solar saltern.BMC microbiology · 2025Article
- Comparative genomics of Bacillus velezensis and Bacillus subtilis reveals distinction and evolution of lipopeptide antimicrobial gene clusters.BMC genomics · 2025Article
- PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.Nature communications · 2025Article
- Genomic and Pathogenic Characterization of Vibrio alginolyticus CG-1 Isolated from Crassostrea gigas.Current microbiology · 2025Article
- Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer.NPJ biofilms and microbiomes · 2025Article
- Whole-Genome analysis of Bacillus subtilis MBBL2 genomic characterization and comparative genomics.Functional & integrative genomics · 2025Article
- Whole genome analysis of Stenotrophomonas geniculata MK2 and antagonism against Botrytis cinerea in strawberry.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01.Scientific reports · 2025Article
- Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance.Antonie van Leeuwenhoek · 2025Article
263 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWith the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains. AVAILABILITY: PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net. CONTACT: junyu@big.ac.cn; xiaojingfa@big.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.