GENOMICS TOOLS UPDATES
1st Aug 2013
The Plant Metabolomic Network, the free online tool which enables users to find and predict genes or proteins, other metabolites, reactions, and pathways, is constantly expanding its output. In June this year seven new databases were released, including BarleyCyc and OryzaCyc. In July, many existing databases were updated – AraCyc 11.5 now contains data on 597 pathways, 9041 enzymes, 3490 interactions, and 2613 compounds. For tutorials, see this page.
Sol Genomics Network, online home to the tomato genome consortium and the tomato genome sequence that was finished last year, have a new set of pages for breeders – the SGN Breeders Toolbox. It includes a database of markers and QTLs, and a phenotype search tool. SGN have also provided Cassava researchers with a new set of databases and tools, found at Cassavabase.org.
KBASE is a new free software and online space from the US Department of Energy. It aims to provide an environment for interdisciplinary research and collaboration, including gene and protein databases for both prokaryotic and eukaryotic systems. For plant scientists, there is a tool for discovering and mapping genetic variations within plant populations. User Home has tutorials, guides, and an introduction.
Medicago researchers will be interested in the Medicago resources from the J. Craig Ventor Institute. Medicago genome v4 was released in July, and users can help annotate your favourite gene family or add your paper to the annotation.