Reference : Mercator: A fast and simple web server for genome scale functional annotation of plan...
Scientific journals : Article
Life sciences : Phytobiology (plant sciences, forestry, mycology...)
http://hdl.handle.net/10993/12488
Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data
English
Lohse, Marc []
Nagel, Axel []
Herter, Thomas []
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Schroda, Michael []
Zrenner, Rita []
Tohge, Takayuki []
Fernie, Alisdair R. []
Stitt, Mark []
Usadel, Bjorn []
2014
Plant, Cell & Environment
Blackwell Publishing
37
5
1250-8
Yes (verified by ORBilu)
International
0140-7791
1365-3040
New York
NY
[en] Functional annotation ; MapMan ; transcriptomics ; genome annoatation ; next-generation sequencing
[en] Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required, to make this 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.
Researchers
http://hdl.handle.net/10993/12488
10.1111/pce.12231
http://onlinelibrary.wiley.com/doi/10.1111/pce.12231/abstract

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