RT Journal Article
SR Electronic
T1 panX: pan-genome analysis and exploration
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 072082
DO 10.1101/072082
A1 Wei Ding
A1 Franz Baumdicker
A1 Richard A. Neher
YR 2017
UL http://biorxiv.org/content/early/2017/07/18/072082.abstract
AB 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 software 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 webserver or by serving panX locally as a browser-based application.