blastn: Wrapper for the NCBI Nucleotide-Nucleotide BLAST

In gschofl/blastr: A wrapper for NCBI Blast

Description

• blastn is the traditional BLASTN requiring an exact match of 11.

• blastn_short is the BLASTN programme optimised for sequences shorter than 50 bases.

• megablast is the traditional megablast used to find very similar sequences (intracpecies or closely related species).

• dc_megablast is discontiguous megablast used to find more distant (e.g. interspecies) sequences.

Usage

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

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

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

dc_megablast(query, db = "nt", 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: nt).
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 at the NCBI servers.

Details

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

Value

A BlastReport or BlastTable object, depending on the value of outfmt.

See Also

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

Other blast functions: blastp, blastp_short, blastp_short; blastx; makeblasttdb; qblast; rpsblast; tblastn; tblastx

Examples

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