A survey of computational methods in transcriptome-wide alternative splicing analysis

Jianbo Wang, Zhenqing Ye, Hui-ming Huang, Huidong Shi, Victor X Jin

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

Original languageEnglish (US)
Pages (from-to)59-66
Number of pages8
JournalBiomolecular Concepts
Volume6
Issue number1
DOIs
StatePublished - Mar 1 2015

Fingerprint

Alternative Splicing
Computational methods
Transcriptome
Software
Genes
RNA Sequence Analysis
Exons
Gene Expression Profiling
RNA
Surveys and Questionnaires
Direction compound

Keywords

  • alternative splicing (AS)
  • differential splicing
  • exon-skipping
  • graph-based exon-skipping scanner (GESS)
  • RNA-sequencing (RNA-seq)

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Cellular and Molecular Neuroscience

Cite this

A survey of computational methods in transcriptome-wide alternative splicing analysis. / Wang, Jianbo; Ye, Zhenqing; Huang, Hui-ming; Shi, Huidong; Jin, Victor X.

In: Biomolecular Concepts, Vol. 6, No. 1, 01.03.2015, p. 59-66.

Research output: Contribution to journalArticle

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