Basic Applied Bioinformatics

CHAPTER 12 Basic Local Alignment Search Tool for Nucleotide (BLASTn)

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

12.1 INTRODUCTION

The Basic Local Alignment Search Tool (BLAST) is a collection of programs for searching homologous sequences for a given query sequence or a set of sequences against selected database (called “Subject sequence”). Thus, BLAST finds regions of local similarities between these query and subject sequences. BLAST is a heuristic program, developed by Altschul and coworkers (Altschul et al., 1990), that can yield results in a reasonable time. The term “heuristic” means that the developed algorithm is faster than the classical method but may not be the optimum method. Default parameters of BLAST can be modified according to need.

BLASTn (BLAST with suffix n) is one of the BLAST programs (Table 12.1) that is used to compare a nucleotide query sequence against a nucleotide database. Functional and evolutionary relationships between sequences can be deciphered using BLAST. In addition, it is used to identify member(s) of gene families.

TABLE 12.1 Overview of various types of BLAST algorithms available at the National Center for Biotechnology Information (NCBI) website, with their applications.

BLAST type	Query	Database	Alignment level	Application
BLASTn	Nucleotide	Nucleotide	Nucleotide	Oligo‐mapping, cross‐species sequence study, cDNA, EST study, screening repetitive elements, gDNA annotation.
BLASTp