DigestDNA: Simulate Restriction Digestion of DNA

Description

Restriction enzymes can be used to cut double-stranded DNA into fragments at specific cut sites. DigestDNA performs an in-silico restriction digest of the input DNA sequence(s) given one or more restriction sites.

Usage

DigestDNA(sites, myDNAStringSet, type = "fragments", strand = "both", processors = 1)

Arguments

sites

A character vector of DNA recognition sequences and their enzymes' corresponding cut site(s).

myDNAStringSet

A DNAStringSet object or character vector with one or more sequences in 5' to 3' orientation.

type

Character string indicating the type of results desired. This should be (an abbreviation of) either "fragments" or "positions".

strand

Character string indicating the strand(s) to cut. This should be (an abbreviation of) one of "both", "top", or "bottom". The top strand is defined as the input DNAStringSet sequence, and the bottom strand is its reverse complement.

processors

The number of processors to use, or NULL to automatically detect and use all available processors.

Value

DigestDNA can return two types of results: cut positions or the resulting DNA fragments corresponding to the top, bottom, or both strands. If type is "positions" then the output is a list with the cut location(s) in each sequence in myDNAStringSet. The cut location is defined as the position after the cut relative to the 5'-end. For example, a cut at 6 would occur between positions 5 and 6, where the respective strand's 5' nucleotide is defined as position 1.If type is "fragments" (the default), then the result is a DNAStringSetList. Each element of the list contains the top and/or bottom strand fragments after digestion of myDNAStringSet, or the original sequence if no cuts were made. Sequences are named by whether they originated from the top or bottom strand, and list elements are named based on the input DNA sequences. The top strand is defined by myDNAStringSet as it is input, whereas the bottom strand is its reverse complement.

Details

In the context of a restriction digest experiment with a known DNA sequence, it can be useful to predict the expected DNA fragments in-silico. Restriction enzymes make cuts in double-stranded DNA at specific positions near their recognition site. The recognition site may be somewhat ambiguous, as represented by the IUPAC_CODE_MAP. Cuts that occur at different positions on the top and bottom strands result in sticky-ends, whereas those that occur at the same position result in fragments with blunt-ends. Multiple restriction sites can be supplied to simultaneously digest the DNA. In this case, sites for the different restriction enzymes may be overlapping, which could result in multiple close-proximity cuts that would not occur experimentally. Also, note that cut sites will not be matched to non-DNA_BASES in myDNAStringSet.

Examples

Run this code

# digest hypothetical DNA sequences with BamHI
data(RESTRICTION_ENZYMES)
site <- RESTRICTION_ENZYMES[c("BamHI")]
dna <- DNAStringSet(c("AAGGATCCAA", "GGGATCAT"))
dna # top strand
reverseComplement(dna) # bottom strand
names(dna) <- c("hyp1", "hyp2")
d <- DigestDNA(site, dna)
d # fragments in a DNAStringSetList
unlist(d) # all fragments as one DNAStringSet

# Restriction digest of Yeast Chr. 1 with EcoRI and EcoRV
data(yeastSEQCHR1)
sites <- RESTRICTION_ENZYMES[c("EcoRI", "EcoRV")]
seqs <- DigestDNA(sites, yeastSEQCHR1)
seqs[[1]]

pos <- DigestDNA(sites, yeastSEQCHR1, type="positions")
str(pos)