BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
NCBI BLAST
Basic Local Alignment Search Tool
From The NCBI Handbook,
Section 16. The BLAST Sequence Analysis Tool, by Tom Madden
Summary
The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA.
Basic Local Alignment Search Tool (BLAST) (1, 2) is the tool most frequently used for calculating sequence similarity. BLAST comes in variations for use with different query sequences against different databases. All BLAST applications, as well as information on which BLAST program to use and other help documentation, are listed on the BLAST homepage. This chapter will focus more on how BLAST works, its output, and how both the output and program itself can be further manipulated or customized, rather than on how to use BLAST or interpret BLAST results.