MassArray (version 1.24.0)

identifySNPs: Identify SNPs

Description

Function to identify potential single nucleotide polymorphisms (SNPs) which allow mapping of a novel peak sequence to the expected amplicon sequence

Usage

identifySNPs(peak.sequence, sequence, rxn = c("T", "C"))

Arguments

peak.sequence

Nucleotide sequence (can also be base composition - ex: "A6G2C1T3") as a character string

sequence

Nucleotide sequence for wildtype/expected amplicon as a character string

rxn

One of "T" or "C" specifying which cleavage reaction to use for SNP analysis

Value

Returns a list of potential SNP matches for the input peak.sequence. Each element of the list contains multiple items as follows:

sequence

corresponds to peak.sequence

position

corresponds to the matched position within sequence

base

corresponds to the altered nucleotide (i.e. "A", "T", "C", "G", or "")

type

corresponds to the class of SNP (i.e. "substitution" or "deletion")

Details

The algorithm steps through the sequence, substituting one nucleotide at a time with the other three base pairs or a blank character (deletion), in order to determine a base compositional match to the input peak.sequence which represents a peak not found in the native sequence.

Examples

## SINGLE SUBSTITUTION
identifySNPs("AAGT","AATTTT")
## MULTIPLE SUBSTITUTION POSSIBILITIES
identifySNPs("A1G1T1","AATTTT")
## DELETION
identifySNPs("AAT","AGATTTT")