rpsblast: Wrapper for the NCBI Reversed Position Specific Blast

In gschofl/blastr: A wrapper for NCBI Blast

Description

Run rpsblast() without arguments to print usage and arguments description.

Usage

rpsblast(query, db = "Cdd", out = NULL, outfmt = "xml", max_hits = 20,
evalue = 10, remote = FALSE, ...)

Arguments

...	Additional parameters passed on to the BLAST commmand line tools. See here for a description of common options.
query	Query sequences as path to a FASTA file, an XStringSet object, or a character vector.
db	The database to BLAST against (default: Cdd).
out	(optional) Output file for alignment. If NULL and the BLAST result is returned as a BlastReport or BlastTable object.
outfmt	Output format, 'xml' or 'table'.
max_hits	How many hits to return (default: 20).
evalue	Expect value cutoff (default: 10).
remote	Execute search remotely.

See Also

Other blast functions: blastn, blastn_short, blastn_short, dc_megablast, dc_megablast, megablast, megablast; blastp, blastp_short, blastp_short; blastx; makeblasttdb; qblast; tblastn; tblastx

Examples

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gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.