Megx.net--database resources for marine ecological genomics - PubMed (original) (raw)

Megx.net--database resources for marine ecological genomics

Thierry Lombardot et al. Nucleic Acids Res. 2006.

Abstract

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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Figures

Figure 1

Figure 1

Fast access to the annotation highlights of marine microorganisms. Here, the archaea-like C1 metabolism key gene is R.baltica.

Figure 2

Figure 2

The Genomes Mapserver. (A) Marine genomes and metagenomic fragments can be browsed and searched on a world map on our web-based system. (B) An example showing a Geographic-BLAST search for genes encoding proteorhodopsins in the currently available dataset.

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