ArticleBioinformatics (Oxford, England)2009
PanCGH: a genotype-calling algorithm for pangenome CGH data.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- Comparative Genome Analysis ofFrontiers in microbiology · 2019Article
- The bacterial pangenome as a new tool for analysing pathogenic bacteria.New microbes and new infections · 2015Article
- A brief review of software tools for pangenomics.Genomics, proteomics & bioinformatics · 2015Review
- Genotypic and phenotypic analysis of dairy Lactococcus lactis biodiversity in milk: volatile organic compounds as discriminating markers.Applied and environmental microbiology · 2013Article
- Explaining microbial phenotypes on a genomic scale: GWAS for microbes.Briefings in functional genomics · 2013Review
- Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.BMC microbiology · 2013Article
- Volatile compound fingerprinting of mixed-culture fermentations.Applied and environmental microbiology · 2011Article
- Comparative phenotypic and molecular genetic profiling of wild Lactococcus lactis subsp. lactis strains of the L. lactis subsp. lactis and L. lactis subsp. cremoris genotypes, isolated from starter-free cheeses made of raw milk.Applied and environmental microbiology · 2011Article
- Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.Microbial biotechnology · 2011Article
- Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.BMC genomics · 2010Article
- PanCGHweb: a web tool for genotype calling in pangenome CGH data.Bioinformatics (Oxford, England) · 2010Article
- Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays.Microbial biotechnology · 2010Article
- Article
- Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures.Genome biology and evolution · 2010Article
- Genomics of dairy fermentations.Microbial biotechnology · 2008Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data.
resultsWe have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis.cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.
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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.