Dataset Information

PanX: pan-genome analysis and exploration.

ABSTRACT: Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.

SUBMITTER: Ding W

PROVIDER: S-EPMC5758898 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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panX: pan-genome analysis and exploration.

Ding Wei W Baumdicker Franz F Neher Richard A RA

Nucleic acids research 20180101 1

Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is cou ...[more]

PMID: 29077859

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Project description:Recent developments of sequencing technologies that allow the production of massive amounts of genomic and genotyping data have highlighted the need for synthetic data representation and pattern recognition methods that can mine and help discovering biologically meaningful knowledge included in such large data sets. Correspondence analysis (CA) is an exploratory descriptive method designed to analyze two-way data tables, including some measure of association between rows and columns. It constructs linear combinations of variables, known as factors. CA has been used for decades to study high-dimensional data, and remarkable inferences from large data tables were obtained by reducing the dimensionality to a few orthogonal factors that correspond to the largest amount of variability in the data. Herein, I review CA and highlight its use by considering examples in handling high-dimensional data that can be constructed from genomic and genetic studies. Examples in amino acid compositions of large sets of species (viruses, phages, yeast, and fungi) as well as an example related to pairwise shared orthologs in a set of yeast and fungal species, as obtained from their proteome comparisons, are considered. For the first time, results show striking segregations between yeasts and fungi as well as between viruses and phages. Distributions obtained from shared orthologs show clusters of yeast and fungal species corresponding to their phylogenetic relationships. A direct comparison with the principal component analysis method is discussed using a recently published example of genotyping data related to newly discovered traces of an ancient hominid that was compared to modern human populations in the search for ancestral similarities. CA offers more detailed results highlighting links between modern humans and the ancient hominid and their characterizations. Compared to the popular principal component analysis method, CA allows easier and more effective interpretation of results, particularly by the ability of relating individual patterns with their corresponding characteristic variables.

Dataset Information

PanX: pan-genome analysis and exploration.

Publications

panX: pan-genome analysis and exploration.

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