Toward a Visualization of DNA Sequences

Abstract

Most biologists associate pattern discovery in DNA with finding repetitive sequences or commonalities across several sequences. However, pattern discovery is not limited to finding repetitions and commonalities. Pattern discovery also involves identifying objects and distinguishing objects from one another. Human vision is unmatched in its ability to identify and distinguish objects. Considerable research into human vision has revealed to a fair degree the visual cues that our brains use to segment an image into separate regions and entities. In this paper, we consider some of these visual cues to construct a novel graphical representation of a DNA sequence. We exploit one of these cues, proximity, to segment DNA into visibly distinct regions and structures. We also demonstrate how to manipulate proximity to identify motifs visually. Lastly, we demonstrate how an additional cue, color, can be used to visualize the Shannon entropy associated with different structures. The presence of large numbers of such regions and structures in DNA suggests that they likely play some important biological role and would be interesting targets for further research. © 2010 Springer Science+Business Media, LLC.