RepetDB

RepetDB manages and catalogs repetitive DNA elements by integrating heterogeneous genomic repeat data with InterMine to support analysis of genomic repeats.

Key Features:

• Data Integration: Utilizes InterMine's flexible data model and data warehouse architecture to integrate heterogeneous biological datasets related to repetitive DNA sequences.
• Customizable Query Facility: Provides a customizable query interface that enables retrieval of specific datasets pertinent to genomic repeats.
• Extensible Framework: Built on InterMine's extensible framework, allowing addition of new tools and features to extend functionality.
• Analysis Tools: Includes a flexible query builder, genomic region search capabilities, and a library of "widgets" that perform statistical analyses of repetitive DNA elements.
• Data Export Options: Supports export of results in multiple commonly used file formats for downstream analysis.
• Web Services and Client Libraries: Exposes web services with client libraries available in five widely-used programming languages.

Scientific Applications:

• Genomic Research: Facilitates studies on the distribution and impact of repetitive sequences within genomes.
• Evolutionary Biology: Supports comparative genomics to investigate the evolutionary dynamics of repeat elements across species.
• Functional Genomics: Enables investigations into how repetitive DNA influences gene regulation and genome stability.

Methodology:

Built on InterMine's data warehouse architecture to support complex data integration from various sources.