PASTA: splice junction identification from RNA-Sequencing data
PASTA: splice junction identification from RNA-Sequencing data
复制标题
DOI：
10.1186/1471-2105-14-116
复制
发表时间：
2013-04-04
影响因子：
3
通讯作者：
Riva, Alberto
中科院分区：
文献类型：
--
作者：
Tang, Shaojun;Riva, Alberto
背景资料：下一代转录组测序（RNA-Seq）正在成为研究选择性剪接及其调控的强大实验工具，但需要专门的分析方法和工具。意大利面（Patterned Alignments for Splicing and Transcriptome Analysis）是一种专门为RNA-Seq数据设计的剪接点检测算法，依靠高度精确的比对策略以及启发式和统计方法的组合，以高精度识别外显子-内含子连接。在真实的和模拟数据集上与TopHat和其他剪接点预测软件的比较表明，PASTA表现出高特异性，敏感性，尤其是在较低的覆盖水平下。此外，PASTA具有高度的可配置性和灵活性，因此可以应用于广泛的分析场景：它能够处理单端和双端读取，它不依赖于典型剪接信号的存在，并且它使用生物体特异性回归模型来准确识别junctions.Conclusions：PASTA是一种高效和灵敏的工具，可以从RNA-Seq数据中识别剪接连接。与类似程序相比，它能够识别更多数量的真实的剪接点，并提供高度注释的输出文件，其中包含有关其位置和特征的详细信息。准确的连接数据反过来又有助于剪接异构体的重建及其表达水平的分析，这将由仍在开发中的PASTA管道的其余模块进行。因此，PASTA的使用可以使转录和选择性剪接的大规模调查成为可能。
Background: Next generation transcriptome sequencing (RNA-Seq) is emerging as a powerful experimental tool for the study of alternative splicing and its regulation, but requires ad-hoc analysis methods and tools. PASTA (Patterned Alignments for Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designed for RNA-Seq data, relying on a highly accurate alignment strategy and on a combination of heuristic and statistical methods to identify exon-intron junctions with high accuracy.Results: Comparisons against TopHat and other splice junction prediction software on real and simulated datasets show that PASTA exhibits high specificity and sensitivity, especially at lower coverage levels. Moreover, PASTA is highly configurable and flexible, and can therefore be applied in a wide range of analysis scenarios: it is able to handle both single-end and paired-end reads, it does not rely on the presence of canonical splicing signals, and it uses organism-specific regression models to accurately identify junctions.Conclusions: PASTA is a highly efficient and sensitive tool to identify splicing junctions from RNA-Seq data. Compared to similar programs, it has the ability to identify a higher number of real splicing junctions, and provides highly annotated output files containing detailed information about their location and characteristics. Accurate junction data in turn facilitates the reconstruction of the splicing isoforms and the analysis of their expression levels, which will be performed by the remaining modules of the PASTA pipeline, still under development. Use of PASTA can therefore enable the large-scale investigation of transcription and alternative splicing.