sapFinder

The software tool 'sapFinder' is an R package for the detection of variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of single amino acid polymorphisms (SAPs) through database searching, post-processing, and generation of an HTML-based report with a visualized interface. 'sapFinder' is implemented as a Bioconductor package in R.

Topic

Proteomics

Detail

  • Operation: Deposition;Query and retrieval

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.18.0

  • Credit: The State Key Development Program for Basic Research of China, the Program of International S&T Cooperation, Guangdong Provincial Engineering Laboratory for Proteomics, Shenzhen Key Laboratory of Transomics Biotechnologies, ShenZhen Engineering Laboratory for Proteomics.

  • Input: -

  • Output: -

  • Contact: xsh.skye@gmail.com;wenbo@genomics.cn

  • Collection: -

  • Maturity: Stable

Publications

  • sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
  • Wen B, et al. sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. 2014; 30:3136-8. doi: 10.1093/bioinformatics/btu397
  • https://doi.org/10.1093/bioinformatics/btu397
  • PMID: 25053745
  • PMC: PMC4609003

Download and documentation

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