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Find all instances of a sequence motif in a genome

Source: R/find_motif_sites.R
findMotifSites.Rd

Searches a genome for all occurrences of a DNA sequence motif on both strands and returns their positions as a GRanges object. This is the bacterial equivalent of CpG island finding — for example, locating all GATC (Dam methyltransferase) sites in an E. coli genome.

Usage

findMotifSites(genome, motif, ...)

Arguments

genome

A DNAStringSet object (Biostrings), a BSgenome object, or a character string giving the path to a FASTA file containing the genome sequence.

motif

A character string specifying the DNA sequence motif to search for (e.g., "GATC" or "CCWGG"). Standard IUPAC ambiguity codes are supported (e.g., W = A or T). The motif is matched exactly on the forward strand; its reverse complement is searched on the minus strand.

...

Additional arguments (currently unused; reserved for future use).

Value

A GRanges object with one range per motif instance. Ranges are 1-based and have width equal to nchar(motif). The mcols column motif records the search motif string.

Details

This function requires the Biostrings package (Bioconductor). If genome is a BSgenome object, BSgenome is also required. Both can be installed with:


  BiocManager::install(c("Biostrings", "BSgenome"))

Palindromic motifs (e.g., GATC) will have both forward and reverse strand hits at each location. Non-palindromic motifs will have distinct forward and reverse hits.

Examples

if (FALSE) { # \dontrun{
# Find all GATC sites in a genome from a FASTA file
gatc_sites <- findMotifSites(genome = "MG1655.fa", motif = "GATC")
} # }

if (FALSE) { # \dontrun{
# With a BSgenome object
library(BSgenome.Ecoli.NCBI.20080805)
gatc_sites <- findMotifSites(genome = BSgenome.Ecoli.NCBI.20080805, motif = "GATC")
} # }