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BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs that explore all of the available sequence databases for protein or DNA. BLAST is the only book completely devoted to this popular and important technology and offers biologists, computational biology students, and bioinformatics professionals a clear understanding of this program. This book shows you how to get specific answers with BLAST and how to use the software to interpret results. BLAST was born in the first months of 1989 at the National Center for Biotechnology Information (NCBI). The BLAST programs have been the fruit of much hard work by scores of talented programmers and scientists. This work continues, linking BLAST output to other databases, improving alignment formatting options, refining the types. Comparisons between the human and mouse genomes show how little has changed since humans and mice last shared a common ancestor around 75 million years ago. Very few genes are unique to humans or mice, and in general the genes are more than 80% identical at the sequence level. However, genes account for a small fraction of these genomes and the majority of sequence is not recognizably similar. This is where BLAST, the Basic Local Alignment Search Tool, comes in. BLAST is useful for finding similarities between biological sequences, be they DNA, RNA, or protein. Sequence similarity is often an indication of conserved function, and you can use comparative sequence analysis to understand biological sequences in much the same way that ancient Greeks used comparative anatomy to understand the human body or that linguists used the Rosetta Stone to understand Egyptian hieroglyphs.