PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics
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Date
Authors
Van Bel, Michiel
Diels, Tim
Vancaester, Emmelien
Kreft, Lukasz
Botzki, Alexander
Van de Peer, Yves
Coppens, Frederik
Vandepoele, Klaas
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is
a plant-oriented online resource for comparative,
evolutionary and functional genomics. The PLAZA
platform consists of multiple independent instances
focusing on different plant clades, while also providing
access to a consistent set of reference species.
Each PLAZA instance contains structural and functional
gene annotations, gene family data and phylogenetic
trees and detailed gene colinearity information.
A user-friendly web interface makes the necessary
tools and visualizations accessible, specific
for each data type. Here we present PLAZA 4.0, the
latest iteration of the PLAZA framework. This version
consists of two new instances (Dicots 4.0 and
Monocots 4.0) providing a large increase in newly
available species, and offers access to updated and
newly implemented tools and visualizations, helping
users with the ever-increasing demands for complex
and in-depth analyzes. The total number of
species across both instances nearly doubles from
37 species in PLAZA 3.0 to 71 species in PLAZA 4.0,
with a much broader coverage of crop species (e.g.
wheat, palm oil) and species of evolutionary interest
(e.g. spruce, Marchantia). The new PLAZA instances
can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians
to optimally leverage the power of the
PLAZA platform.
Description
Supplementary Data are available at NAR Online.
Keywords
PLAZA, Wheat, Palm oil, Application programming interface, Bioinformatics, Comparative gene mapping, Conceptual framework, Data processing, Gene function, Genetic conservation, Marchantia, Nonhuman, Online system, Phylogeny, Plant genome
Sustainable Development Goals
Citation
Van Bel, M., Diels, T., Vancaester, E. et al. 2018, 'PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics', Nucleic Acids Research, vol. 46, pp. D1190–D1196.