A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

Methods Mol Biol. 2017:1533:183-200. doi: 10.1007/978-1-4939-6658-5_10.

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/ .

Keywords: Comparative genomics; Gene family; Gene functions; Orthology; Plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Databases, Genetic*
  • Genes, Plant
  • Genetic Markers
  • Genome, Plant*
  • Genomics* / methods
  • Molecular Sequence Annotation
  • Multigene Family
  • Phylogeny
  • Plants / classification
  • Plants / genetics*
  • Software*
  • User-Computer Interface
  • Web Browser

Substances

  • Genetic Markers