MetaProx: the database of metagenomic proximons

Area of Science:

• Bioinformatics
• Metagenomics
• Systems Biology

Background:

• Metagenomic research often lacks homology-dependent functional information.
• Identifying functional gene clusters (operons) in metagenomes is challenging.
• Traditional relational databases may not be optimal for semistructured biological data.

Purpose of the Study:

• Introduce MetaProx, a database of metagenomic proximons.
• Facilitate research on metagenomic functional interactions and networks.
• Explore alternative data representations for biological data management.

Main Methods:

• Defined proximons as contiguous, co-directional genes with close intergenic distances.
• Developed a searchable repository of proximon objects.
• Implemented a 'Data as Data' policy using serialized objects for database, search, and user files.

Main Results:

• MetaProx contains 4,210,818 proximons and 8,926,993 member genes.
• Proximons serve as significant metagenomic operon candidates.
• The database enables homology-independent inference of functional linkages.

Conclusions:

• MetaProx accelerates metagenomic functional interaction studies.
• The 'Data as Data' approach offers an efficient alternative for biological data representation.
• MetaProx is a valuable resource for exploring metagenomic functional networks.