title: Ten years of pan-genome analyses.
abstract: Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impact and limits, and we propose possible extensions, including analyses at the whole genome multiple sequence alignment level.
authors.affiliation: Novartis (Hellas) S.A.C.I., 12th Km Athens-Lamia North Road, 14451 Metamorfossi, Athens, Greece.
authors.forename: George
authors.initials: G
authors.lastname: Vernikos
authors.affiliation: Novartis Vaccines Research, Via Fiorentina 1, 53100 Siena, Italy.
authors.forename: Duccio
authors.initials: D
authors.lastname: Medini
authors.affiliation: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Riley
authors.affiliation: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA. Electronic address: tettelin@som.umaryland.edu.
authors.forename: Hervé
authors.initials: H
authors.lastname: Tettelin
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D064349:Genome, Microbial; D023281:Genomics / Q000379:methods* / Q000639:trends; D006801:Humans; D016415:Sequence Alignment / Q000379:methods