Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.
Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.
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DOI：
10.2174/1389202918666170215125048
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发表时间：
2017-06
期刊：
影响因子：
2.6
通讯作者：
Bai Y
中科院分区：
文献类型：
--
作者：
Ding L;Rath E;Bai Y
选择性剪接（alternative splicing，AS）是一种转录后过程，它能从同一基因产生不同的转录产物，并在环境刺激下产生不同的蛋白质产物。AS发生在mRNA序列上的特定位点，其中一些已被确定。已经开发了多种生物信息学工具来从实验数据中检测AS。 这篇综述的目的是帮助研究人员使用特定的工具来帮助他们的研究，并在这些先前建立的工具的基础上开发新的AS检测工具。 我们选择了最近发表的15种AS检测工具;我们从几个方面对它们进行了分类和描述。此外，这些工具与相同的启动输入的性能进行了比较。 我们回顾了这些工具的以下分类功能：出版信息，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，映射到多个位置的读数，异构体注释基础，精确检测的AS类型和性能基准。 通过对这些工具的比较，我们提供了一个全景的优势和各自的适用范围的不足之处。
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.