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.

Package details

AuthorXiao Chen [aut, cre] (<https://orcid.org/0000-0001-5059-8846>)
Bioconductor views Alignment Annotation Software
MaintainerXiao Chen <seanchen607@gmail.com>
LicenseArtistic-2.0
Version1.0.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FScanR")

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FScanR documentation built on Nov. 8, 2020, 5:26 p.m.