Cite as: Cold Spring Harb. Protoc.; 2007; doi:10.1101/pdb.ip41

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Steps Used by the BLAST Algorithm

David W. Mount

Adapted from "Sequence Database Searching for Similar Sequences," Chapter 6, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

The BLAST algorithm performs DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. BLAST is very popular due to availability of the program on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide a set of very powerful search tools for the molecular biologist that are freely available to run on many computer platforms. This article provides a list of steps that describe how the BLAST algorithm searches a sequence database.


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D. W. Mount
Studies of Varying Alignment Algorithm, Amino Acid Scoring Matrix, and Gap Penalties
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D. W. Mount
Using PAM Matrices in Sequence Alignments
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