xmapbridge

xmapbridge maps reporters from Affymetrix exon arrays to X:Map genome browser annotations for human, mouse, and rat to support exon-level genome annotation and analysis.

Key Features:

• Comprehensive coverage: Targets known and predicted exons from Affymetrix exon arrays across human, mouse, and rat, including non-coding transcribed regions.
• Precision in annotation: Associates each array reporter with specific genomic features to enable accurate exon-level mapping and to account for alternative splicing.
• BioConductor integration: Integrates with the BioConductor package to support downstream data analysis and visualization workflows.
• Plotting-file export: Exports plotting files compatible with the X:Map genome browser to enable visualization of mapped reporters.

Scientific Applications:

• Gene and genome structure analysis: Links array reporters to genomic features to support detailed study of gene structure and regulatory elements.
• Alternative splicing studies: Provides exon-level mappings suitable for investigation of alternative splicing across protein-coding genes.
• Non-coding RNA research: Covers non-coding transcribed regions to facilitate analysis of non-coding RNA roles in gene regulation and expression.

Methodology:

Exports plotting files compatible with the X:Map genome browser and associates each Affymetrix exon array reporter with corresponding genomic features for visualization and annotation.