FScanR

an R package to detect Programmed Ribosomal Frameshifting (PRF) events from mRNA/cDNA

‘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.

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 see Tutorial.

:gear: Install FScanR in R (>= 3.5.0)

library(devtools)
install_github("seanchen607/FScanR")
library(FScanR)

What is Programmed Ribosomal Frameshifting (PRF)?

• From Mauger et al., 2013, FEBS Letters

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.

Authors

Xiao CHEN, PhD

Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York

https://www.researchgate.net/profile/Xiao_Chen126

If you use 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.