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

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Computational Biology / methods*
  • Internet
  • Molecular Sequence Annotation
  • Software*