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 transcriptionregulation 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 [http://www.ncbi. nlm.nih.gov/BLAST/]. 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 [http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html] or interpret BLAST results.
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