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Nucleic Acids Research 2006 34(Database Issue):D390-D393; doi:10.1093/nar/gkj070
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Nucleic Acids Research, 2006, Vol. 34, Database issue D390-D393
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Megx.net—database resources for marine ecological genomics

Thierry Lombardot1, Renzo Kottmann1, Hauke Pfeffer1, Michael Richter1, Hanno Teeling1, Christian Quast1 and Frank Oliver Glöckner1,2,*

1Microbial Genomics Group, Max Planck Institute for Marine Microbiology D-28359 Bremen, Germany 2International University Bremen D-28759 Bremen, Germany

*To whom correspondence should be addressed. Tel: +49 0421 2028938; Fax: +49 0421 2028580; Email: fog{at}mpi-bremen.de

Received August 8, 2005. Revised October 8, 2005. Accepted October 8, 2005.

Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts. Megx.net includes (i) a geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; (ii) an environmental genome browser with fast search functionalities; (iii) a database with precomputed analyses for selected complete genomes; and (iv) a database and tool to classify metagenomic fragments based on oligonucleotide signatures. These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at http://www.megx.net.


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