blast {blaster}

Runs BLAST sequence comparison algorithm.

Description

Runs BLAST sequence comparison algorithm.

Usage

blast(
  query,
  db,
  maxAccepts = 1,
  maxRejects = 16,
  minIdentity = 0.75,
  alphabet = "nucleotide",
  strand = "both",
  output_to_file = FALSE
)

Arguments

query

A dataframe of the query sequences (containing Id and Seq columns) or a string specifying the FASTA file of the query sequences.

db

A dataframe of the database sequences (containing Id and Seq columns) or a string specifying the FASTA file of the database sequences.

maxAccepts

A number specifying the maximum accepted hits.

maxRejects

A number specifying the maximum rejected hits.

minIdentity

A number specifying the minimal accepted sequence similarity between the query and hit sequences.

alphabet

A string specifying the query and database alphabet: 'nucleotide' or 'protein'. Defaults to 'nucleotide'.

strand

A string specifying the strand to search: 'plus', 'minus' or 'both'. Defaults to 'both'. Only affects nucleotide searches.

output_to_file

A boolean specifying the output type. If TRUE, the results are written into a temporary file a string containing the file name and location is returned. Otherwise a dataframe of the results is returned. Defaults to FALSE.

Value

A dataframe or a string. A dataframe is returned by default, containing the BLAST output in columns QueryId, TargetId, QueryMatchStart, QueryMatchEnd, TargetMatchStart, TargetMatchEnd, QueryMatchSeq, TargetMatchSeq, NumColumns, NumMatches, NumMismatches, NumGaps, Identity and Alignment. A string is returned if 'output_to_file' is set to TRUE. This string points to the file containing the output table.

Examples

query <- system.file("extdata", "query.fasta", package = "blaster")
db <- system.file("extdata", "db.fasta", package = "blaster")

blast_table <- blast(query = query, db = db)

query <- read_fasta(filename = query)
db <- read_fasta(filename = db)
blast_table <- blast(query = query, db = db)

prot <- system.file("extdata", "prot.fasta", package = "blaster")
prot_blast_table <- blast(query = prot, db = prot, alphabet = "protein")