Previously, we presented a system called Alignment Viewer that uses information visualization techniques to visualize similarities between a single DNA sequence and a large database of other sequences [Chi et al. , IEEE Visualization ’95, pp. 44–51, IEEE CS (1995); Chi et al. , IEEE Visualization ’96, pp. 133–140 and 477, IEEE CS (1996)]. In this paper, we extend, summarize, and describe the system using several interesting case studies. We present our comb glyph technique for visualizing alignments between sequences. In this paper, we also extend the original system by incorporating computational steering, and the visualization of differences between data sets. The case studies and the new extended system present our approach of extracting significant relationships in the biological data set. © 2000 SPIE and IS&T.