annmap

annmap maps Affymetrix exon array reporters to genomic features and provides coordinate-based queries and visualization for exon- and gene-level analysis in human, mouse, and rat genomes.

Key Features:

• Annotation Mapping: Provides detailed mappings that associate Affymetrix exon array reporters with specific genomic features, including known and predicted exons in protein-coding and non-coding regions.
• Coordinate-Based Queries: Supports queries by genomic coordinates to retrieve information about specific regions for deep sequencing and read-mapping analyses.
• API-Driven Database Access: Exposes programmatic functions such as genesInRange(), geneToExon(), and exonDetails() to query gene ranges, map genes to exons, and obtain exon-level data.
• Visualization Tools: Includes functions to plot gene architecture and to visualize sequencing data from BAM files.
• Integration with Ensembl Data: Leverages underlying annotations from Ensembl to provide up-to-date genome annotation information.

Scientific Applications:

• Alternative Splicing Analysis: Enables mapping of exon-level probes to support the identification and analysis of alternative splicing events.
• Non-Coding RNA Research: Facilitates investigation of non-coding regions targeted by exon arrays for studies of non-coding RNA function.
• Genomic Data Visualization: Supports visualization of gene architecture and aligned sequencing reads to aid interpretation of genomic and transcriptomic data.

Methodology:

Built on the X:Map genome annotation database and Ensembl annotations; exposes API functions (genesInRange(), geneToExon(), exonDetails()); provides plotting of gene architecture and BAM file data and is available as a BioConductor package.