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Environmental and meta-genomics - a bioinformatic system to detect and assign functions to habitat specific gene patterns

Objective

More than 99% of the microbial diversity on earth still resists cultivation. To exploit this nearly inexhaustible natural resource of new genes and functions direct cloning and sequencing of large DNA fragments from the environment (the metagenome) is the ongoing goal of many researchers worldwide. Nevertheless, more than 50 to 70% of the genes currently found on the genomes and metagenomes lack functional assignments, representing so called hypothetical genes. This shortcoming will be addressed by our new integrative approach that correlates possible gene functions by taking into account habitat specific data and global patterns of gene distribution. First approaches to map biodiversity of cultivated microorganisms and correlate it with ecological and geogr aphical data have already been published, but without genomic data. Independently, the existence of clusters of genes across genomes is documented. No methodology or database integrates these two kinds of information in a single concept at this time. There fore the time is ripe to develop a new integrative system combining genomic and ecological data by using Geographic Information Systems (GIS) in a "Metagenomes Mapserver". The project will result in a new basic technology to systematically store, analyse, visualize and evaluate ecological, geographical and genomic data together. A proof of usefulness will already be given in the proposed project, as data on the carbon and sulfur-cycles will be linked with genomic data from specific sites to predict gene pat terns with potential functions involved in these globally important processes. This proposal is ideally suited for the high risk/high impact NEST program as it cuts across several scientific disciplines and only a few institutes worldwide can develop such a system (high risk). Once it has been installed and its usefulness proven, new areas of scientific development in data mining for environmental monitoring and biotechnology will be possible (high impact)

Field of science

  • /natural sciences/earth and related environmental sciences/physical geography/cartography/geographic information systems
  • /natural sciences/computer and information sciences/data science/data mining

Call for proposal

FP6-2003-NEST-A
See other projects for this call

Funding Scheme

NoE - Network of Excellence

Coordinator

MAX-PLANCK-GESELLSCHAFT ZUR FOERDERUNG DER WISSENSCHAFTEN E.V.; REPRESENTED BY MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY
Address
Hofgartenstrasse 8
Muenchen
Germany

Participants (3)

POZNAN UNIVERSITY OF TECHNOLOGY
Poland
Address
Pl. Marii Sklodowskiej-curie 5
Poznan
UNIVERSITE DE GENEVE
Switzerland
Address
24 Rue Du General Dufour
Geneve 4
VEREIN ZUR FÖRDERUNG DES TECHNOLOGIETRANSFERS AN DER HOCHSCHULE BREMERHAVEN E.V
Germany
Address
An Der Karlstadt 10
Bremerhaven