Rapid Identification of Single Nucleotide Substitutions Using SeqDoC

Abstract

Identification and characterization of nucleotide substitutions in DNA sequences for single nucleotide polymorphism or point mutation detection can be a time consuming and sometimes inaccurate process, particularly in relatively low-throughput situations where fully automated solutions may not be appropriate. SeqDoC provides a simple web-based application to simplify this identification process, by using direct subtractive comparison of the raw sequence traces to highlight differences characteristic of nucleotide substitutions. Sequencing artefacts, such as variable peak separation and signal strength, are compensated for with moving window normalisation functions, whereas the signal to noise ratio of the comparison trace is greatly enhanced by applying an algorithm to emphasise features associated with nucleotide substitutions. Analysis of the output is simple and intuitive, permitting rapid identification of points of difference between the reference and test sequence traces.