Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
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.
Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, China.
Qi
Q
Liu
Chong
C
Chen
Enjian
E
Shen
Fangqing
F
Zhao
Zhongsheng
Z
Sun
Jinyu
J
Wu
D017398:Alternative Splicing / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D058977:Molecular Sequence Annotation; D012984:Software