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Review
. 2017 Jun;18(3):268-277.
doi: 10.2174/1389202918666170215125048.

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data

Lizhong Ding  1 , Ethan Rath  1 , Yongsheng Bai  1   2
Affiliations
Review

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data

Lizhong Ding et al. Curr Genomics. 2017 Jun.

Abstract

Background: Alternative splicing (AS) is a posttranscriptional process that produces differ-ent transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been de-fined. Multiple bioinformatics tools have been developed to detect AS from experimental data.

Objectives: The goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools.

Method: We selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted.

Result: We reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks.

Conclusion: Through comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.

Keywords: Alternative splicing; RNA-seq; Read-split-run; Read-split-walk; Splice junctions detection; Spliceosome.

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Figures

Fig. (1)
Fig. (1)
Examples of classical AS events: the alternatively spliced exons are denoted by boxes filled with various colors. Constitutive exons are denoted by blue boxes. Green arrows point out alternative 3’ splice site position. Black arrows point out the 5’ splice sites position. The figure is adapted from [16]. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this paper.)
See this image and copyright information in PMC

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