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.

Visualization of Biomedical Data

“…But we are struggling to develop effective visual analysis strategies because no single visual metaphor captures the richness of population-level data. Pan-genome visualizations, designed to show core and accessory genes in a species' genome, are dashboards that combine existing methods (94). Phylogeography uses maps to show phylogenetic relationships across geocoded samples (95).…”

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

“…Default values for the prior probabilities were inferred from a published study of core genes across multiple bacterial species [3]. We account for 1% of random deletions of core genes, which gives p c = 0.99.…”

Visualization of Biomedical Data

“…But we are struggling to develop effective visual analysis strategies because no single visual metaphor captures the richness of population level data. Pan-genome visualizations, designed to show core and 'accessory' genes in a species' genome, are dashboards that combine existing methods (92). Phylogeography uses maps to show phylogenetic relationships across geocoded samples (93).…”