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sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Bioinformatics

November 2014

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.

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.

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