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

'FScanR' identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX homolog sequence alignment between targeted genomic/cDNA/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of 'FScanR' and should be in a tabular format with 14 columns. For BLASTX, the output parameter should be: -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe'. For diamond BLASTX, the output parameter should be: -outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe qframe.

Getting started

Package details

Bioconductor views Alignment Annotation Software
Maintainer
LicenseArtistic-2.0
Version0.99.7
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("seanchen607/FScanR")
seanchen607/FScanR documentation built on Sept. 13, 2020, 5:42 p.m.