blast: Run BLAST search

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Run BLAST search

Description

Run BLAST search

Usage

blast(
  query,
  db,
  type = "blastn",
  evalue = 1e-06,
  output_format = "tabular",
  args = NULL,
  ungapped = FALSE,
  quiet = FALSE,
  multithread = FALSE,
  remove_db_gaps = TRUE
)

Arguments

query	(Required) Query sequence. Accepts a DNABin object, DNAStringSet object, Character string, or filepath.
db	(Required) Reference sequences to conduct search against. Accepts a DNABin object, DNAStringSet object, Character string, or filepath. If DNAbin, DNAStringSet or character string is provided, a temporary fasta file is used to construct BLAST database. If db is set to "remote", this will conduct a search against NCBI nucleotide database.
type	(Required) type of search to conduct, default 'blastn'
evalue	(Required) Minimum evalue from search
output_format	The output format to be returned. Default is tabular, which returns 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcov See https://www.ncbi.nlm.nih.gov/books/NBK279684/ for custom formatting information
args	(Optional) Extra arguments passed to BLAST
ungapped	Whether ungapped alignment should be conducted. Default is FALSE.
quiet	(Optional) Whether progress should be printed to console, default is FALSE
multithread	Whether multithreading should be used, if TRUE the number of cores will be automatically detected, or provided a numeric vector to manually set the number of cores to use
remove_db_gaps	Whether gaps should be removed from the fasta file used for the database. Note that makeblastdb can fail if there are too many gaps in the sequence.

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.