get.orf <- function(dna.str) {
	# Find positions of codons
	start.codon.pos <- start(matchPattern('ATG', dna.str))
	end.codon.pos <- c(start(matchPattern('TAA', dna.str)),
	start(matchPattern('TAG', dna.str)),
	start(matchPattern('TGA', dna.str)))
	# Get reading frames for codons
	start.codon.frame <- start.codon.pos %% 3
	end.codon.frame <- end.codon.pos %% 3
	# Find the corresponding end for a given start codon
	# Add two to the end position to include end codon
	orf.ends <-
	sapply(1:length(start.codon.pos),
	function(xx) min(end.codon.pos[end.codon.frame == start.codon.frame[xx]
	& end.codon.pos > start.codon.pos[xx]])) + 2
	# Build IRanges output and delete invalid elements
	IRanges(start.codon.pos[orf.ends != Inf], orf.ends[orf.ends != Inf])
	}

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