R: Runs BLAST sequence comparison algorithm.

blast {blaster} | R Documentation

## 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")

[Package blaster version 1.0.4 Index]