title: PLAZA: a comparative genomics resource to study gene and genome evolution in plants.
abstract: The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.
authors.affiliation: Department of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium. sebastian.proost@psb.vib-ugent.be
authors.forename: Sebastian
authors.initials: S
authors.lastname: Proost
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Bel
authors.forename: Lieven
authors.initials: L
authors.lastname: Sterck
authors.forename: Kenny
authors.initials: K
authors.lastname: Billiau
authors.forename: Thomas
authors.initials: T
authors.lastname: Van Parys
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
mesh_terms: D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D005810:Multigene Family; D010802:Phylogeny; D014584:User-Computer Interface