BLAST

In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence. Background BLAST, which The New York Times called the Google of biological research, is one of the most widely used bioinformatics programs for sequence searching. It addresses a fundamental problem in bioinformatics research. The heuristic algorithm it uses is much faster than other approaches, such as calculating an optimal alignment. This emphasis on speed is vital to making the algorithm practical on the huge genome databases currently available, although subsequent algorithms can be even faster. Before BLAST, FASTA was developed by David J. Lipman and William R. Pearson in 1985. Lipman later went on to lead the development of BLAST, recruiting four other scientists-Stephen Altschul, Warren Gish, Webb Miller, and Eugene Myers-to create the final program. BLAST extended the alignment work in FASTA by adding a novel stochastic model developed by Samuel Karlin and Stephen Altschul. They proposed "a method for estimating similarities between the known DNA sequence of one organism with that of another", and their work has been described as "the statistical foundation for BLAST." Subsequently, Altschul, Gish, Miller, Myers, and Lipman designed and implemented the BLAST program, which was published in the Journal of Molecular Biology in 1990 and has been cited over 100,000 times since.