ABSTRACT
Acknowledgments.................................................................................................... 35 References................................................................................................................ 35
Many of our colleagues and customers work in pharmaceutical or academic research departments that include a focus on drug-target identification and validation. If you were to walk down the hallways of these organizations and look inside the offices and conference rooms at the whiteboards, you would likely see drawings representing nucleotide or protein sequences and their associated subsequences of interest. Many of the subsequences are represented by patterns. Nucleotide sequences are typically drawn as straight lines, with the patterns drawn as boxes, ovals, or underlines. See figure 5.5, showing the functional anatomy of a gene, for a good example of this. Protein sequences are often shown as two-dimensional objects based on their known or conjectured secondary structure.
