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A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

Part of the Methods in Molecular Biology book series (MIMB,volume 1533)

Abstract

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/.

Key words

  • Gene family
  • Orthology
  • Gene functions
  • Comparative genomics
  • Plants

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Acknowledgments

I thank Michiel Van Bel for excellent technical assistance and maintenance of the PLAZA platform, all long-term PLAZA users for their feedback and Annick Bleys for help in preparing the manuscript. This work was supported by the Multidisciplinary Research Partnership “Bioinformatics: From Nucleotides to Networks” Project (no 01MR0410W) of Ghent University.

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Correspondence to Klaas Vandepoele .

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Vandepoele, K. (2017). A Guide to the PLAZA 3.0 Plant Comparative Genomic Database. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_10

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