WheatMine

WheatMine provides integrated querying and analysis of wheat genomic data to support interpretation of the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 and related wheat genomics research.

Key Features:

• Data Integration: Integrates diverse genomic data types into an InterMine-based unified database for wheat genomics, including IWGSC RefSeq v1.0.
• Customizable Query Facility: Implements a fast, flexible query builder that supports complex queries across large datasets.
• Genomic Region Search: Supports targeted searches of specific genomic regions and coordinates within the wheat genome.
• Statistical Analysis Tools: Includes a library of "widgets" that perform statistical analyses on query results.
• Data Export Options: Exports query and analysis results in numerous commonly used file formats for downstream analyses.
• Extensibility and Customization: Built on an extensible InterMine framework that allows addition of new data types, tools, and modules.
• Web Services and Client Libraries: Provides web services and client libraries in five programming languages for programmatic access and integration.

Scientific Applications:

• Reference-based wheat genomics: Enables analysis and interpretation of genomic data aligned to IWGSC RefSeq v1.0.
• Genetic variation and gene function analysis: Facilitates exploration of genetic variation and gene function within the wheat genome.
• Comparative and evolutionary genomics: Supports investigation of evolutionary relationships among wheat genes and genomic regions.
• Trait discovery and breeding research: Assists in identifying genomic regions and candidate genes relevant to crop trait studies.

Methodology:

Built on the InterMine framework to construct large-scale biological databases from heterogeneous data sources, with a modular design enabling integration of additional data types, query capabilities, analysis widgets, and export functionality.