GeneFarm

GeneFarm provides homogeneous, traceable structural and functional annotations for Arabidopsis nuclear genes and their corresponding gene products to support consistent genome annotation and downstream genomic analyses.

Key Features:

• Family-wide annotation approach: Leverages similarities within gene families to extrapolate features from one gene to others in the same family, increasing annotation consistency.
• Advanced prediction tools: Applies gene structure and function prediction tools to perform complete annotation procedures.
• Integrated database (GeneFarm): Stores documented and traceable annotations in the GeneFarm database as a centralized resource.
• Extensive coverage: Contains annotations for over 3,000 genes distributed across more than 300 gene families.
• Collaborative expert network: Engages 16 partner laboratories contributing expert-curated annotations for specific gene families.
• Swiss-Prot integration: Maintains an ongoing collaboration with the Swiss Institute of Bioinformatics to integrate GeneFarm data into the Swiss-Prot protein knowledgebase.

Scientific Applications:

• Improved genome annotation: Produces homogeneous, reliable annotations of Arabidopsis nuclear genes to enhance genome annotation quality.
• Genomic data mining: Provides annotated gene structures and functions to support mining and comparative analysis of genomic sequences.
• Experimental planning and design: Supplies documented and traceable gene and protein annotations to inform experimental design.
• Investigation of genetic networks and pathways: Facilitates exploration of genetic networks and pathways through family-level functional annotation.

Methodology:

Annotations are generated using a family-wide approach that extrapolates features across gene families and by applying gene structure and function prediction tools; annotated data are stored in the GeneFarm database and are being prepared for integration into Swiss-Prot.