Perceptual principles for scalable sequence alignment visualization

Sequence comparison is a fundamental task in the biological sciences. Scientists often need to understand the similarities and differences between genetic sequences to understand evolution, to infer common function, or identify differences. Because the sequences are too long for manual examination, scientists rely on alignment tools that automatically identify subsequences that match between the sequences being compared. Numerous approaches for displaying and exploring alignments exist, and have been incorporated into a wide variety of tools. See [Procter et al. 2010] for a survey of several existing approaches.