blastx: Wrapper for the NCBI Translated Query-Protein Subject BLAST

In gschofl/blastr: A wrapper for NCBI Blast

Description

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

Usage

blastx(query, query_gencode = 1, db = "nr", out = NULL, outfmt = "xml",
 max_hits = 20, evalue = 10, matrix = "BLOSUM62", 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.
query_gencode	Genetic code used to translate the query (default: 1).
db	The database to BLAST against (default: nr).
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).
matrix	Scoring matrix name (default: BLOSUM62).
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; makeblasttdb; qblast; rpsblast; tblastn; tblastx

Examples

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