sapFinder：一种用于在鸟枪法蛋白质组学实验中检测变异肽的 R/Bioconductor 包。
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
机构信息
BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China.
BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China BGI-Shenzhen, Shenzhen 518083, China, Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia and Macau University of Science and Technology, Taipa, Macau 999078, China.
出版信息
Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397. Epub 2014 Jul 22.
UNLABELLED
Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface.
AVAILABILITY AND IMPLEMENTATION
sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license.
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位于阅读框内的单核苷酸变异 (SNV) 可导致单个氨基酸多态性 (SAP)，从而导致相应氨基酸序列以及蛋白质功能的改变。在实验和生物信息学水平的蛋白质组学分析中，准确检测 SAP 是一个重要问题。在此，我们提出了 sapFinder，这是一个用于基于串联质谱 (MS/MS) 的蛋白质组学数据检测变异肽的 R 软件包。该软件包自动从公共 SNV 存储库或样本特异性下一代测序 (NGS) 数据构建与变异相关的数据库，并通过数据库搜索、后处理以及生成带有可视化界面的基于 HTML 的报告来识别 SAP。
可用性和实现
sapFinder 作为 R 中的 Bioconductor 包实现。该软件包和示例可以在 http://bioconductor.org/packages/devel/bioc/html/sapFinder.html 下载，根据 GPL-2 许可证提供。
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