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.
