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a catalog of biological databases

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Database information

PLAZA (An online platform for plant comparative genomics)

General information

Description: PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface.
Year founded: 2009
Last update: 2017
Version: v4.0
Accessibility:
Manual:
Accessible
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Country/Region: Belgium
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Ghent University
Address: Technologiepark 927, Ghent, Belgium
City: Ghent
Province/State:
Country/Region: Belgium
Contact name (PI/Team): Klaas Vandepoele
Contact email (PI/Helpdesk): klaas.vandepoele@psb.vib-ugent.be

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-11-30]
Lina Ma [2018-06-05]
zhang yang [2018-01-27]
Shixiang Sun [2016-03-25]
Shixiang Sun [2015-11-21]
Shixiang Sun [2015-06-28]
Shixiang Sun [2015-06-26]

Ranking

All databases:
248/4549 (94.57%)
Gene genome and annotation:
96/1211 (92.155%)
Phylogeny and homology:
14/190 (93.158%)
248
Total Rank
315
Citations
28.636
z-index

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Publications

29069403
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. [PMID: 29069403]
Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K.

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.

Nucleic Acids Res. 2018:46(D1) | 27 Citations (from Europe PMC, 2020-02-08)
27987171
A Guide to the PLAZA 3.0 Plant Comparative Genomic Database. [PMID: 27987171]
Vandepoele K.

PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/ .

Methods Mol Biol. 2017:1533() | 1 Citations (from Europe PMC, 2020-02-08)
25324309
PLAZA 3.0: an access point for plant comparative genomics. [PMID: 25324309]
Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K.

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 well-characterized 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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 141 Citations (from Europe PMC, 2020-02-15)
20040540
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. [PMID: 20040540]
Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K.

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.

Plant Cell. 2009:21(12) | 146 Citations (from Europe PMC, 2020-02-15)