MetaMine - A tool to detect and analyse gene patterns in their environmental context

Background: Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities alone. Extending similarity searches with gene pattern approaches, defined as genes sharing a distinct genomic neighbourhood, have shown to significantly improve the number of functional assignments. Further functional evidences can be gained by correlating these gene patterns with prevailing environmental parameters. MetaMine was developed to approach the large pool of unclassified proteins by searching for recurrent gene patterns across habitats based on key genes. Results: MetaMine is an interactive data mining tool which enables the detection of gene patterns in an environmental context. The gene pattern search starts with a user defined environmentally interesting key gene. With this g...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank Oliver Glöckner
• Keywords: BMCBI 2008, Gene Patterns, Graphical User Interface, Key Gene