sapFinder
Computational Tool
FAIR Metrics
0 evaluations
General Information
DescriptionAn R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments
Homepagehttp://bioconductor.org/packages/devel/bioc/html/sapFinder.html
Publications
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments
Bo Wen; Shaohang Xu; Gloria M. Sheynkman; Qiang Feng; Liang Lin; Quanhui Wang; Xun Xu; Jun Wang; Siqi Liu
Summary: 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.
Contact: siqiliu@genomics.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btu397
Metrics:
4
Canned Analyses generated by the tool
There are no indexed analyses by this tool at the moment.
Datasets analyzed by the tool
There are no indexed analyses by this tool at the moment.
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.