RNA-Seq: Detection, annotation and visualization of alternative splicing from RNA-Seq

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Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.

Genomics. 2011 Dec 28;

Authors: Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J

Abstract
Alternative splicing is a crucial mechanism by which diverse gene products can be generated from a limited number of genes, and is thought to be involved in complex orchestration of eukaryotic gene expression. Next-generation sequencing technologies, with reduced time and cost, provide unprecedented opportunities for deep interrogation of alternative splicing at the genome-wide scale. In this study, an integrated software SplicingViewer has been developed for unambiguous detection, annotation and visualization of splice junctions and alternative splicing events from RNA-Seq data. Specifically, it allows easy identification and characterization of splice junctions, and holds a versatile computational pipeline for in-depth annotation and classification of alternative splicing with different patterns. Moreover, it provides a user-friendly environment in which an alternative splicing landscape can be displayed in a straightforward and flexible manner. In conclusion, SplicingViewer can be widely used for studying alternative splicing easily and efficiently. SplicingViewer can be freely accessed at http://bioinformatics.zj.cn/splicingviewer.


PMID: 22226708 [PubMed - as supplied by publisher]



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