Lohse Marc, Nagel Axel, Herter Thomas, May Patrick, Schroda Michael, Zrenner Rita, Tohge Takayuki, Fernie Alisdair R, Stitt Mark, Usadel Björn
Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
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 http://mapman.gabipd.org/web/guest/app/Mercator.
下一代技术产生了海量的基因序列数据。需要高效的注释工具才能使这些数据适用于功能基因组学分析。Mercator管道可自动为蛋白质或核苷酸序列赋予功能术语。它使用MapMan“BIN”本体，该本体是为植物“组学”数据的功能注释量身定制的。分类过程会对参考数据库进行并行序列搜索，汇编结果并为每个查询计算最可能的MapMan BIN。在当前版本中，该管道依赖于源自三种参考生物（拟南芥、衣藻、水稻）、具有经过审核的SwissProt注释的各种其他植物物种以及InterPro、CDD和KOG的2000多个蛋白质结构域和家族图谱的人工策划参考分类。与人工注释相比，Mercator预测的功能注释准确率超过90%。除了可直接用于可视化软件MapMan的映射文件外，Mercator还提供图形概述图、在便捷的网页浏览器界面中的详细注释信息以及一个MapMan到GO的转换表，以便将结果导出为GO术语。可通过http://mapman.gabipd.org/web/guest/app/Mercator免费获取Mercator。
