HOLLYWOOD: a comparative relational database of alternative splicing

Area of Science:

• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing (AS) generates diverse mRNA and protein isoforms from a single gene, complicating gene expression studies.
• Developing effective databases for AS research is a significant challenge.
• Integrating genomic annotation, splicing regulatory elements, and cross-species ortholog information is crucial for comprehensive AS analysis.

Purpose of the Study:

• To develop the Hollywood system, a relational database designed to support AS research.
• To integrate accurate exon and splice site annotation with splicing regulatory elements and predicted AS events.
• To link splicing information for orthologous genes across different species.

Main Methods:

• Genomic annotation of splicing patterns derived from cDNA and expressed sequence tag alignments.
• Integration of splice site characteristics, regulatory elements (enhancers, silencers), and conserved/non-conserved splicing patterns.
• Implementation as a relational database with a web query tool and graphical visualization, compatible with the UCSC Genome Browser.

Main Results:

• The Hollywood system provides comprehensive AS information for human and mouse.
• It enables searches for exons with specific splicing characteristics or regulatory element composition.
• Graphical representations of gene splicing patterns are available and can be overlaid on the UCSC Genome Browser.

Conclusions:

• The Hollywood system offers a valuable resource for investigating alternative splicing.
• It facilitates the analysis of splicing patterns, regulatory elements, and cross-species comparisons.
• The database and its query tool enhance experimental and computational AS research.