Concepts and History
Sequence alignment is a fundamental procedure that compares two or more biological sequences (whether DNA, RNA, or protein). This chapter introduces the concepts and history of sequence alignment by describing the dynamic programming approach, common basic algorithms, methods, and statistical approaches that have been fundamental to the development of sequence alignment software. It examines the biological concept of homology in detail. The biological goal of alignment is the inference of site homology. Homology is similarity in a character or trait due to inheritance from a common ancestor. The chapter also describes the fundamental difference between the biological and computational goals for which algorithms are generally designed.
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