Sequence Alignment
Résumé
This chapter focuses on comparing sequences using alignment. Sequence alignment is the operation that consists of matching two or more sequences, in order to highlight their similarity, whether it is local or global. If the alignment is given, then computing a score is a relatively simple task. However, if two sequences are given, knowing the best alignment(s) in the sense that they will maximize the score becomes more difficult. Exact alignment algorithms are efficient for small sequences , but their time is unfortunately quadratic, and they are not capable of aligning too large sequences. Consequently, the genome alignment of a few tens or hundreds of megabases should therefore be avoided. A heuristic does not guarantee to find the best or all solutions to a given problem, but achieves at best the construction of a potentially suboptimal solution, or a subset of solutions among those that can ideally be obtained.