Run BLAST search

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.