Protocol

Bioinformatics

Volume 452 of the series Methods in Molecular Biology™ pp 179-197

Bioinformatics Detection of Alternative Splicing

  • Namshin KimAffiliated withMolecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California
  • , Christopher LeeAffiliated withMolecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California

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Abstract

In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter reviews the data, methodology, and technical challenges of these genome-wide analyses of alternative splicing, and briefly surveys some of the uses to which such alternative splicing databases have been put. For example, with proper alternative splicing database schema design, it is possible to query genome-wide for alternative splicing patterns that are specific to particular tissues, disease states (e.g., cancer), gender, or developmental stages. EST alignments can be used to estimate exon inclusion or exclusion level of alternatively spliced exons and evolutionary changes for various species can be inferred from exon inclusion level. Such databases can also help automate design of probes for RT-PCR and microarrays, enabling high throughput experimental measurement of alternative splicing.

Key words

alternative splicing genome annotation alternative donor alternative acceptor exon skipping intron retention tissue-specific cancer-specific exon inclusion exon exclusion RT-PCR microarray