README.md

In seanchen607/FScanR: Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

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)

:orange_book: 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.

:pencil2: 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.

seanchen607/FScanR documentation built on April 7, 2022, 4:50 p.m.