AphidBase

AphidBase provides centralized genomic data and curated annotations for the pea aphid (Acyrthosiphon pisum) to support community-driven genome annotation and genetic research.

Key Features:

• Organized genomic repository: Centralized access to genomic data and curated annotations for the pea aphid genome.
• Consortium development: Developed by the International Aphid Genomics Consortium (IAGC).
• GMOD-based implementation: Constructed using open-source Generic Model Organism Database (GMOD) components.
• Apollo genome editor: Integrates Apollo for collaborative curation and editing of gene models.
• GBrowse visualization: Uses GBrowse for visualization and exploration of genomic features and architecture.
• BLAST search: Provides BLAST (Basic Local Alignment Search Tool) for sequence similarity searches.
• Full-text search: Includes a full-text search engine for retrieval of database content.
• Community wiki: Maintains a wiki to support communication and coordination among researchers involved in annotation.

Scientific Applications:

• Community genome annotation: Supports collaborative annotation and curation of pea aphid gene models.
• Aphid genetic research: Enables genetic studies and investigations into aphid biology using curated genomic data.
• Genomic visualization: Facilitates exploration of genomic architecture and feature relationships via GBrowse.
• Comparative and similarity analyses: Enables sequence similarity searches and related analyses using BLAST.

Methodology:

Built with GMOD components and integrating Apollo and GBrowse, plus BLAST and a full-text search engine, with an accompanying wiki for community coordination.