# FScanR: an R package to detect Programmed Ribosomal Frameshifting (PRF) events from mRNA/cDNA [](https://github.com/seanchen607/FScanR) [](http://www.repostatus.org/#active) ‘FScanR’ identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX output in tab format containing the best hits of targeted mRNA/cDNA sequences against the peptide library of the same species or a close relative. <a href="https://doi.org/10.1111/1755-0998.13023"><img src="docs/schematic.png" height="100" align="center" /></a> To acquire the input file with 14 columns in tab-delimited format, which is generated by BLASTX, parameters should be used for BLASTX: -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe' For details, please visit <https://doi.org/10.1111/1755-0998.13023>. ## :gear: Install FScanR in R (>= 3.5.0) library(devtools) install_github("seanchen607/FScanR") library(FScanR) ## :orange_book: What is Programmed Ribosomal Frameshifting (PRF)? <a href="https://doi.org/10.1016/j.febslet.2013.03.002"><img src="docs/Structural-diversity.png" height="400" align="center" /></a> - From [*Mauger et al., 2013, FEBS Letters*](https://doi.org/10.1016/j.febslet.2013.03.002) Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation that results in the production of multiple, unique proteins from a single mRNA. The process can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary, 3-dimensional mRNA structure. It has been described mainly in viruses (especially retroviruses), retrotransposons and bacterial insertion elements, and also in some cellular genes. For details, please visit [Ribosomal frameshift](https://en.wikipedia.org/wiki/Ribosomal_frameshift). ## :pencil2: Authors Xiao CHEN, PhD Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York <https://www.researchgate.net/profile/Xiao_Chen126> [](https://twitter.com/intent/tweet?hashtags=FScanR&url=https://github.com/seanchen607/FScanR&screen_name=SC607) If you use [FScanR](https://github.com/seanchen607/FScanR) in published research, please cite the most appropriate paper(s) from this list: 1. **X Chen**, Y Jiang, F Gao^\*, W Zheng, TJ Krock, NA Stover, C Lu, LA Katz & W Song (2019). Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors. ***Molecular Ecology Resources***, 19(5):1292-1308. doi: [10.1111/1755-0998.13023](https://doi.org/10.1111/1755-0998.13023).