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PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van Bel (UGent) , Tim Diels (UGent) , Emmelien Vancaester (UGent) , Lukasz Kreft (UGent) , Alexander Botzki (UGent) , Yves Van de Peer (UGent) , Frederik Coppens (UGent) and Klaas Vandepoele (UGent)
(2018) NUCLEIC ACIDS RESEARCH. 46(D1). p.D1190-D1196
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Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
MULTIPLE SEQUENCE ALIGNMENT, MAXIMUM-LIKELIHOOD PHYLOGENIES, DATA, VISUALIZATION, ACCURACY, PLATFORM, VIEWER, TREE, TOOL

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Citation

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Chicago
Van Bel, Michiel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, and Klaas Vandepoele. 2018. “PLAZA 4.0 : an Integrative Resource for Functional, Evolutionary and Comparative Plant Genomics.” Nucleic Acids Research 46 (D1): D1190–D1196.
APA
Van Bel, M., Diels, T., Vancaester, E., Kreft, L., Botzki, A., Van de Peer, Y., Coppens, F., et al. (2018). PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics. NUCLEIC ACIDS RESEARCH, 46(D1), D1190–D1196.
Vancouver
1.
Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, et al. PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics. NUCLEIC ACIDS RESEARCH. 2018;46(D1):D1190–D1196.
MLA
Van Bel, Michiel, Tim Diels, Emmelien Vancaester, et al. “PLAZA 4.0 : an Integrative Resource for Functional, Evolutionary and Comparative Plant Genomics.” NUCLEIC ACIDS RESEARCH 46.D1 (2018): D1190–D1196. Print.
@article{8558157,
  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.},
  author       = {Van Bel, Michiel and Diels, Tim and Vancaester, Emmelien and Kreft, Lukasz and Botzki, Alexander and Van de Peer, Yves and Coppens, Frederik and Vandepoele, Klaas},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {MULTIPLE SEQUENCE ALIGNMENT,MAXIMUM-LIKELIHOOD PHYLOGENIES,DATA,VISUALIZATION,ACCURACY,PLATFORM,VIEWER,TREE,TOOL},
  language     = {eng},
  number       = {D1},
  pages        = {D1190--D1196},
  title        = {PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics},
  url          = {http://dx.doi.org/10.1093/nar/gkx1002},
  volume       = {46},
  year         = {2018},
}

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