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sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen, B, Xu, S, Sheynkman, GM, Feng, Q, Lin, L, Wang, Q, Xu, X, Wang, J, Liu, S
Bioinformatics (Oxford, England). 2014;(21):3136-8
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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.