Bo Wen1, Shaohang Xu1, Gloria M Sheynkman1, Qiang Feng2, Liang Lin1, Quanhui Wang2, Xun Xu1, Jun Wang3, Siqi Liu2. 1. 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. 2. 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. 3. 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 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, Ch
Abstract
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.
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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