SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

Bioinformatics. 2012 Sep 15;28(18):2385-7. doi: 10.1093/bioinformatics/bts452. Epub 2012 Jul 20.


Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing and identifies potential functional changes that result from splice variation. It displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.

Availability and implementation: SpliceSeq is freely available at http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. The application is a Java program that can be launched via a browser or installed locally. Local installation requires MySQL and Bowtie.

Contact: mryan@insilico.us.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Alternative Splicing*
  • Computer Graphics
  • Sequence Analysis, RNA / methods*
  • Software*