Interactive visualisation of oligomer frequency in DNA

Abstract

Since 1990, bioinformaticians have been exploring applications of the Chaos Game Representation (CGR) for visualisation, statistical characterisation and comparison of DNA sequences. We focus on the development of a new computational algorithm and description of new software tool that enables CGR visualisation of frequencies of K-mers (oligomers) in a flexible way such that it is possible to visualise the whole genome or any of its parts (like genes), and parallel comparison of several sequences, all in real time. User can interactively specify the size and position of visualised region of the DNA sequence, zoom in or out, and change parameters of visualisation. The tool has been written in JAVATM language and is freely available to public.