bioconductor-fscanr
Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
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Description
'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.
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Summary
Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output
Last Updated
Jul 7, 2023 at 14:10
License
Artistic-2.0
Total Downloads
11.8K
Supported Platforms
noarch