What is the Portal for Marine Ecological GenomiX?
The megx.net portal for Marine Ecological GenomiX is a web site for specialized georeferenced databases and tools for the analysis of marine bacterial, archaeal, and phage genomes and metagenomes.
The megx.net database, MegDB (microbial ecological genomics DataBase), is a collection of publicly available georeferenced marine bacterial and archaeal genomes and metagenomes, including the Global Ocean Sampling (GOS) reads.
We offer reports compliant with the newly developed Genomic Contextual Data Markup Language (GCDML; Kottmann et al., 2008 ), which implements the new "Minimal Information about Genome/Metagenome Sequence" (MIGS/MIMS; Field, et al., 2008 ) standards.
One of the key elements of megx.net is the Genes Mapserver (developed within the frame of the EU-funded project MetaFunctions ), which facilitates the interpretation of the sequence data in MetaStorage in its environmental context via a browsable world map. The unique strength of the Genes Mapserver is its Global Information System (GIS), which integrates environmental data layers extracted from the World Ocean Atlas (WOA). Currently, 'on the fly' interpolated data include temperature, salinity, dissolved oxygen, apparent oxygen utilization, percent oxygen saturation, phosphate, silicate, and nitrate at standard depths, averaged over annual, seasonal, and monthly periods for any location in the marine system.
In addition to the browser, Geographic-BLAST can be used to query the genome and metagenome databases we offer. You can then view the distribution of georeferenced BLAST hits and use the Mapserver's functionality at any one of these locations.
Megx.net now covers diversity analysis by integrating the SILVA ribosomal RNA databases. SILVA offers comprehensive, quality controlled and aligned 16/18S and 23/28S rRNA sequence databases for in depth phylogenetic reconstruction and diversity analysis.
- Incorporation of MetaBar, through which researchers can manage their own sampling campaigns by combining the megx.net GIS data with self-collected GPS positions.
megx.net was published in the 2010 NAR Database Issue:
Megx.net: integrated database resource for marine ecological genomics Renzo Kottmann; Ivalyo Kostadinov; Melissa Beth Duhaime; Pier Luigi Buttigieg; Pelin Yilmaz; Wolfgang Hankeln; Jost Waldmann; Frank Oliver Glockner Nucleic Acids Res. 2009[Pubmed Abstract] [Free full text]
Additional usability information is available on our FAQ pages.
Renzo Kottmann, Ivalyo Kostadinov, Melissa Beth Duhaime, Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Jost Waldmann, Frank Oliver Glöckner. Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res. 2009 [Pubmed Abstract] [Free full text]
Kottmann R, Gray T, Murph S, Kagan L, Kravitz S, Lombardot T, Field D, Glöckner FO; and the Genomic Standards Consortium. A Standard MIGS/MIMS Compliant XML Schema: Toward the Development of the Genomic Contextual Data Markup Language (GCDML) OMICS. 2008 Jun;12(2):115-21.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I ,Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
The minimum information about a genome sequence (MIGS) specification . Nat. Biotechnol. 2008 May;26(5):541-7.
Lombardot T, Kottmann R , Pfeffer H, Richter M, Teeling H, Quast C, Glöckner FO.
Megx.net -- database resources for marine ecological genomics. Nucleic Acids Res. 2006 Jan 1;34 (Database issue): D390-393.
now extensionurl = //gms-dev.megx.net/map