9 Genomic Techniques and How to Apply Them to Marine Questions
355
of recent marine genomics projects and databases that are trying to catalogue these
new data. This list is not exhaustive.
• Moore
Marine
Microbial
Genome
Sequencing
Project
(http://
www.moore.org/microgenome/). The Moore Foundation’s Microbial Genome
Sequencing Project was launched in April 2004. More information about the
sequencing project can be found at https://research.venterinstitute.org/moore/.
• The Megx.net (http://www.megx.net) database resource for marine ecological
genomics provides specialized databases and tools for genome-wide analyses of
marine bacteria and metagenomics.
• The Marine Genomics Project, Charleston South Carolina (http://
www.marinegenomics.org/). The Marine Genomics pipeline automates the
processing, maintenance, storage, and analysis of ESTs (Expressed Sequence
Tags) or 16S RNA sequences and microarray experiments from 35 different
marine species.
• Marine Genomics Europe or MGE (http://www.marine-genomics-europe.org/)
is devoted to the development, utilization and spreading of high-throughput
approaches for the investigation of the biology of marine organisms. Within
the bioinformatics platform located at Bielefeld University, a bioinformatics
portal (http://www.cebitec.uni-bielefeld.de/brf/cooperations/mge.html) has been
created for the Marine Genomics Europe (MGE) community that provides a central access point for all data sets and various software tools (e.g. GenDB, SAMS,
EMMA).
(c) wwPDB
The Protein Data Bank (PDB) was founded in 1971 at Brookhaven National
Laboratory (Long Island, USA) to archive experimentally determined threedimensional structures of biological macromolecules. In 1974, 12 structures with
atomic coordinates were available. Nowadays the PDB contains the coordinates and
related information of more than 50,000 structures determined using X-ray crystallography, Nuclear Magnetic Resonance (NMR) and electron microscopy techniques
(Henrick et al. 2008).
The importance of protein structures Although the protein structure is more
difficult to determine than protein sequence, representative structures are currently known for about 2,000 protein families. Structures are more conserved than
sequences and often reveal evolutionary relationships hidden at the sequence level.
Structural data is also essential for providing detailed insights into a protein’s
function, catalytic mechanism and interactions with other proteins. Because of the
increase in the number of deposited structures during the last 10 years and because
of structural genomics projects emerging that will generate a large number of 3D
structures, a worldwide protein data bank was needed to maintain a single archive
of publicly available macromolecular structural data.
The worldwide Protein Data Bank (wwPDB) was thus established in 2003
(Berman et al. 2003). The founding members are RCSB PDB (USA), the macromolecular structure database (MSD) at the EBI (Europe), and the Protein Data Bank
355
of recent marine genomics projects and databases that are trying to catalogue these
new data. This list is not exhaustive.
• Moore
Marine
Microbial
Genome
Sequencing
Project
(http://
www.moore.org/microgenome/). The Moore Foundation’s Microbial Genome
Sequencing Project was launched in April 2004. More information about the
sequencing project can be found at https://research.venterinstitute.org/moore/.
• The Megx.net (http://www.megx.net) database resource for marine ecological
genomics provides specialized databases and tools for genome-wide analyses of
marine bacteria and metagenomics.
• The Marine Genomics Project, Charleston South Carolina (http://
www.marinegenomics.org/). The Marine Genomics pipeline automates the
processing, maintenance, storage, and analysis of ESTs (Expressed Sequence
Tags) or 16S RNA sequences and microarray experiments from 35 different
marine species.
• Marine Genomics Europe or MGE (http://www.marine-genomics-europe.org/)
is devoted to the development, utilization and spreading of high-throughput
approaches for the investigation of the biology of marine organisms. Within
the bioinformatics platform located at Bielefeld University, a bioinformatics
portal (http://www.cebitec.uni-bielefeld.de/brf/cooperations/mge.html) has been
created for the Marine Genomics Europe (MGE) community that provides a central access point for all data sets and various software tools (e.g. GenDB, SAMS,
EMMA).
(c) wwPDB
The Protein Data Bank (PDB) was founded in 1971 at Brookhaven National
Laboratory (Long Island, USA) to archive experimentally determined threedimensional structures of biological macromolecules. In 1974, 12 structures with
atomic coordinates were available. Nowadays the PDB contains the coordinates and
related information of more than 50,000 structures determined using X-ray crystallography, Nuclear Magnetic Resonance (NMR) and electron microscopy techniques
(Henrick et al. 2008).
The importance of protein structures Although the protein structure is more
difficult to determine than protein sequence, representative structures are currently known for about 2,000 protein families. Structures are more conserved than
sequences and often reveal evolutionary relationships hidden at the sequence level.
Structural data is also essential for providing detailed insights into a protein’s
function, catalytic mechanism and interactions with other proteins. Because of the
increase in the number of deposited structures during the last 10 years and because
of structural genomics projects emerging that will generate a large number of 3D
structures, a worldwide protein data bank was needed to maintain a single archive
of publicly available macromolecular structural data.
The worldwide Protein Data Bank (wwPDB) was thus established in 2003
(Berman et al. 2003). The founding members are RCSB PDB (USA), the macromolecular structure database (MSD) at the EBI (Europe), and the Protein Data Bank