Basic Local Alignment Search Tool (Blast) and Multiple Sequence Alignment

This chapter look at the topic of pairwise sequence comparison by describing the Basic Local Alignment Search Tool (BLAST). It discusses multiple sequence alignment programs with an emphasis on the first popular program of this class–Cluster Alignment Weighted (ClustalW). In the 1990s, advances in DNA sequencing technology led to a significant expansion of the number of sequences deposited in databases. The chapter examines the logic of how BLAST aligns a query sequence with a subject sequence from a database. It emphasizes the significant advantages of BLAST over other sequence alignment programs: its increased speed and its use of a statistical measurement, the E-value, to assess the significance of the similarity score. The chapter then shifts to look into major BLAST programs available through NCBI. It then analyses the logic of how ClustalW aligns multiple sequences, then considers other multiple sequence alignment programs.