Sequence Similarity and Database Searching

Database searching is perhaps the fastest, cheapest, and most powerful experiment a biologist can perform. No other 10-s test allows a biologist to reveal so much about the function, structure, location or origin of a gene, protein, organelle, or organism. A database search does not consume any reagents or require any specific wet-bench laboratory skills; just about anyone can do it, but the key is to do it correctly. The power of database searching comes from not only the size of today’s sequence databases (now containing more than 700,000 annotated gene and protein sequences), but from the ingenuity of certain key algorithms that have been developed to facilitate this very special kind of searching. Given the importance of database searching it is crucial that today’s life scientists try to become as familiar as possible with the details of the process. Indeed, the intent of this chapter to provide the reader with some insight and historical background to the methods and algorithms that form the foundation of a few of the most common database searching techniques. There are many strengths, misconceptions and weaknesses to these simple but incredibly useful computer experiments.