Novel techniques of graphical representation and analysis of DNA sequences - A review

The advent of automated DNA sequencing techniques has led to an explosive growth in the number and length of DNAs sequenced from different organisms. While this has resulted in a large accumulation of data in the DNA databases, it has also called for the development of suitable techniques for rapid viewing and analysis of the data. Over the last few years several methods have been proposed that address these issues and represent a DNA sequence in a compact graphical form in one-, two-or three-dimensions that can be expanded as necessary to help visualize the patterns in gene sequences and aid in in-depth analysis. Graphical techniques have been found to be useful in highlighting focal and global base dominances, to identify regions of extensive repetitive sequences, differentiate between coding and non-coding regions, and to be indicative of evolutionary divergences. Analysis with graphical methods have also provided insights into new structures in DNA sequences such as fractals and long range correlations, and some measures have been developed that help quantify the visual patterns. This review presents a comprehensive study of the graphical representation methods and their applications in viewing and analysing long DNA sequences and evaluates the merits of each of these from a practical viewpoint with prescriptions on domains of applicability of each method. A discussion on the comparative merits and demerits of the various methods and possible future developments have also been included.