GeeFu

GeeFu manages and stores draft genome assemblies and associated genomic feature annotations to support versioned assembly tracking, visualization, and programmatic access for analyses of short-read assembly data.

Key Features:

• Data Management: Stores and tracks multiple versions of genomic assemblies and associated feature annotations in a centralized feature database.
• Assembly Support: Handles draft genome assemblies produced by short-read assembly methods.
• Visualization Tools: Integrates AnnoJ for interactive visualization of genomic feature data.
• Data Access and Sharing: Provides a web-service interface and an API accessible via Ruby scripts and supports feature data stored in BAM files.
• Collaborative Platform: Facilitates sharing of genomic assemblies and annotations among researchers for coordinated analysis.
• Implementation: Implemented using Ruby on Rails as the underlying application framework.

Scientific Applications:

• Gene Prediction: Supports management and review of assemblies and annotations used in gene prediction workflows.
• Comparative Genomics: Enables storage and comparison of multiple assembly versions and feature annotations for comparative analyses.
• PCR Primer Design: Provides annotated assembly data useful for designing PCR primers and other molecular biology assays.

Methodology:

Operates on a feature database implemented in Ruby on Rails, exposes a web-service API and direct Ruby script access, integrates AnnoJ for visualization, supports feature data in BAM files, and stores multiple versions of draft genome assemblies produced by short-read assembly methods.