Visualizing relationships between nucleic acid sequences using correlation images.

This paper describes a portable software package implementing a variation of the dot-matrix plot for genetic sequence comparison in conjunction with highly interactive image manipulation and examination techniques. Visualization is a qualitative method of analyzing and exploring data by presenting data in a pictorial form with an effective interface. Visualization techniques can be applied to molecular sequence comparisons to highlight both the similarities and the differences in a qualitative and descriptive manner. The method used for displaying the sequence comparisons is the correlation image (CI). Among the topics explored in this paper are the generation of correlation images, filtering CIs to visually enhance certain sequence relationships, the handling of large correlation images, and providing an effective interface for the manipulation and exploration of the sequences and their resulting images.