EasyGDB

EasyGDB provides a framework for creating genomic data management web platforms that integrate BLAST-based sequence search, genome browsers, annotation search and download, gene expression visualization, and support for multiple genome versions and annotation datasets.

Key Features:

• Species and project metadata: Incorporates general information about species, projects, and team members as metadata.
• BLAST search: Supports BLAST (Basic Local Alignment Search Tool) for sequence alignment and database searches.
• Genome browsers: Provides genome browsers for visual exploration of genomic sequences.
• Annotation search: Enables annotation searches to query gene annotations.
• Gene expression visualization: Includes tools for visualization of gene expression data.
• Sequence and annotation downloads: Offers file download options for genomic data, annotations, and sequences.
• Gene ID and ortholog lookup: Provides lookup features for gene identifiers and orthologs.
• Support for multiple genome versions and annotation datasets: Accommodates multiple genome assemblies and annotation sets within the platform.
• BLAST databases for storage and retrieval: Employs BLAST databases to store and retrieve sequence data within gene annotation pages.
• JSON metadata customization: Uses JSON files to customize and configure metadata.

Scientific Applications:

• Sequence similarity searches: Perform sequence alignment and similarity searches using BLAST.
• Genomic visualization: Visualize genomic sequences and annotations via genome browsers.
• Annotation querying and retrieval: Search, retrieve, and download gene annotations and sequences.
• Gene expression analysis visualization: Visualize and inspect gene expression data linked to annotations.
• Orthology and identifier resolution: Lookup orthologs and resolve gene identifiers across datasets.
• Management of multiple assemblies and annotations: Host and manage multiple genome versions and annotation datasets for comparative or project-specific use.

Methodology:

Uses BLAST databases for sequence storage and retrieval and JSON files for metadata customization.