Springer Protocols: Abstract: 10. Reconstruction of Full-Length Isoforms from Splice Graphs

10. Reconstruction of Full-Length Isoforms from Splice Graphs

By: Yi Xing³, Christopher Lee⁴

Abstract

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Most alternative splicing events in human and other eukaryotic genomes are detected using sequence fragments produced by high throughput genomic technologies, such as EST sequencing and oligonu-cleotide microarrays. Reconstructing full-length transcript isoforms from such sequence fragments is a major interest and challenge for computational analyses of pre-mRNA alternative splicing. This chapter describes a general graph-based approach for computational inference of full-length isoforms.

Affiliation(s): (3) Department of Internal Medicine, Carver College of Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA
(4) Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA

Book Title: Bioinformatics: Data, Sequence Analysis and Evolution

Series: Methods in Molecular Biology | Volume: 452 | Pub. Date: May-01-2008 | Page Range: 199-205 | DOI: 10.1007/978-1-60327-159-2_10

Subject: Bioinformatics

Key Words: alternative splicing - splice graph - ESTs - microarray - dynamic programming - sequence assembly

References

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