Alignments and Approximate String Matching

The alignments constitute one of the processes used to compare strings. They allow to visualize the resemblance between strings. This chapter deals with several methods that perform the comparison of two strings in this sense. The extension to comparison methods of more than two strings is delicate, leads to algorithms whose execution time is at least exponential, and is not treated here.

The alignments are based on notions of distance or of similarity between strings. The computations are usually performed by dynamic programming. A typical example is the computation of the longest subsequence common to two strings since it shows the algorithmic techniques to implement in order to obtain an efficient computation. In particular, the reduction of the memory space obtained by one of the algorithms constitute a strategy that can often be applied in the solutions to close problems.