Chapter 5 - Pairwise sequence alignment

Abstract

Alignment algorithms are commonly employed in molecular biology for comparing DNA or amino acid sequences. Sequence comparison is the core of bioinformatics study. It's a key first step to examine the structural and functional aspects of newly identified sequences. Comparisons between sequences are becoming increasingly important, since new biological sequences have been created exponentially, enabling a new protein to be found in the database with a functional and evolutionary inference. The two sequence alignment approach is called the pairwise sequence alignment and forms the basis for searching for similarities in the database. This is the way to compare sequences through the search for common patterns of character and to establish a link between similar sequences among residences. Two types of alignment procedures exist, i.e. global alignment and local alignment. The ultimate objective of pairwise sequence alignment is to determine the best pairing of two sequences in order to maximise residue correspondence. This chapter will address briefly on pairwise sequence alignment methods and algorithms.