Affordable Access

deepdyve-link
Publisher Website

PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Authors
  • Proost, Sebastian
  • Van Bel, Michiel
  • Sterck, Lieven
  • Billiau, Kenny
  • Van Parys, Thomas
  • Van de Peer, Yves
  • Vandepoele, Klaas
Type
Published Article
Journal
The Plant Cell
Publisher
American Society of Plant Biologists
Publication Date
Dec 01, 2009
Volume
21
Issue
12
Pages
3718–3731
Identifiers
DOI: 10.1105/tpc.109.071506
PMID: 20040540
Source
Medline
License
Unknown

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.

Report this publication

Statistics

Seen <100 times