Ding Lizhong, Rath Ethan, Bai Yongsheng
Department of Biology.
The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN, USA.
Curr Genomics. 2017 Jun;18(3):268-277. doi: 10.2174/1389202918666170215125048.
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.
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.
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.
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.
Through comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.
可变剪接（Alternative splicing，AS）是一种转录后过程，它从同一基因产生不同的转录本，并且对于响应环境刺激产生多样的蛋白质产物很重要。可变剪接发生在mRNA序列的特定位点，其中一些位点已经被确定。已经开发了多种生物信息学工具来从实验数据中检测可变剪接。
本综述的目的是帮助研究人员使用特定工具辅助他们的研究，并基于这些先前建立的工具开发新的可变剪接检测工具。
我们选择了最近发表的15种可变剪接检测工具；我们在几个方面对它们进行了分类和描述。此外，还对这些工具使用相同起始输入进行了性能比较。
我们回顾了这些工具的以下分类特征：发表信息、工作原理、通用和独特的工作流程、运行平台、输入数据要求、测序深度依赖性、映射到多个位置的 reads、异构体注释基础、精确检测到的可变剪接类型以及性能基准。
通过对这些工具的比较，我们全面展示了每个工具的优点和缺点及其应用范围。
