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

被引：25

作者：

Liu, Qi ^{[1
]}

Chen, Chong ^{[1
]}

Shen, Enjian ^{[1
]}

Zhao, Fangqing ^{[2
]}

Sun, Zhongsheng ^{[1
,2
]}

Wu, Jinyu ^{[1
]}

机构：

[1] Wenzhou Med Coll, Inst Genom Med, Wenzhou 325035, Peoples R China

[2] Chinese Acad Sci, Beijing Inst Life Sci, Beijing 100101, Peoples R China

来源：

GENOMICS | 2012年 / 99卷 / 03期

基金：

中国国家自然科学基金;

关键词：

Next-generation sequencing; Transcriptome; RNA-Seq; Alternative splicing; Soft; Visualization; JUNCTIONS; TOOL; ALIGNMENTS; ULTRAFAST;

D O I：

10.1016/j.ygeno.2011.12.003

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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. (C) 2012 Elsevier Inc. All rights reserved.

引用

页码：178 / 182

页数：5

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