PLAZA 3.0 : an access point for plant comparative genomics
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Date
Authors
Proost, Sebastian
Van Bel, Michiel
Vaneechoutte, Dries
Van de Peer, Yves
Inze, Dirk
Mueller-Roeber, Bernd
Vandepoele, Klaas
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
Comparative sequence analysis has significantly altered
our view on the complexity of genome organization
and gene functions in different kingdoms.
PLAZA 3.0 is designed to make comparative
genomics data for plants available through
a user-friendly web interface. Structural and functional
annotation, gene families, protein domains,
phylogenetic trees and detailed information about
genome organization can easily be queried and visualized.
Compared with the first version released
in 2009, which featured nine organisms, the number
of integrated genomes is more than four times
higher, and now covers 37 plant species. The
new species provide a wider phylogenetic range
as well as a more in-depth sampling of specific
clades, and genomes of additional crop species are
present. The functional annotation has been expanded
and now comprises data from Gene Ontology,
MapMan, UniProtKB/Swiss-Prot, PlnTFDB and
PlantTFDB. Furthermore, we improved the algorithms
to transfer functional annotation from wellcharacterized
plant genomes to other species. The
additional data and new features make PLAZA 3.0
(http://bioinformatics.psb.ugent.be/plaza/) a versatile
and comprehensible resource for users wanting
to explore genome information to study different aspects
of plant biology, both in model and non-model
organisms.
Description
Keywords
PLAZA 3.0, Comparative genomics, Comparative sequence analysis, Plant biology
Sustainable Development Goals
Citation
Proost, S, Van Bel, M, Vaneechoutte, D, Van De Peer, Y, Inze, D, Mueller-Roeber, B & Vandepoele, K 2015, 'PLAZA 3.0 : an access point for plant comparative genomics', Nucleic Acids Research, vol. 43, no. (D1), pp. D974-D981.