blastp: Wrapper for the NCBI Protein-Protein BLAST

In gschofl/blastr: A wrapper for NCBI Blast

Description

• blastp is the traditional BLASTP.

• blastp_short is BLASTP optimised for residues shorter than 30.

Usage

blastp(query, db = "nr", out = NULL, outfmt = "xml", max_hits = 20,
 evalue = 10, matrix = "BLOSUM62", remote = FALSE, ...)

blastp_short(query, 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.
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.

Details

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

See Also

BLAST documentation at http://www.ncbi.nlm.nih.gov/books/NBK1763/.

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

Examples

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