Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Plant Cell Environ. 2014 May;37(5):1250-8. doi: 10.1111/pce.12231. Epub 2013 Dec 17.


Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via

Keywords: MapMan; genome annotation; next-generation sequencing; transcriptomics.

MeSH terms

  • Arabidopsis / genetics
  • Base Sequence
  • Chlamydomonas / genetics
  • Databases, Genetic*
  • Gene Ontology
  • Genome, Plant / genetics*
  • Internet*
  • Molecular Sequence Annotation / methods*
  • Oryza / genetics
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Software*
  • User-Computer Interface


  • Plant Proteins