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

By Marc Lohse, Axel Nagel, T. Herter, P. May, M. Schroda, R. Zrenner, Takayuki Tohge, Alisdair R. Fernie, Mark Stitt, Björn Usadel. Plant, Cell and Environment, 2014

537 citations recorded by the source corpus.

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 http://mapman.gabipd.org/web/guest/app/Mercator.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6590728a5ab5826e0acb5bb4faa0152124cf7913

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “The tool Mercator was therefore developed to allow automatic annotation of plant protein sequences with MapMan terms (Lohse et al., 2014).”