An Overview of Sequence Comparison Algorithms in Molecular Biology*

Molecular biologists frequently compare biosequences to see if any similarities can be found in the hope that what is true of one sequence either physically or functionally is true of its analogue. Such comparisons are made in a variety of ways, some via rigorous algorithms, others by manual means, and others by a combination of these two extremes. The topic of sequence comparison now has a rich history dating back over two decades. In this survey we review the now classic and most established technique: dynamic programming. Then a number of interesting variations of this basic problem are examined that are specifically motivated by applications in molecular biology. Finally, we close with a discussion of some of the most recent and future trends.