The Basic Local Alignment Search Tool, BLAST, finds regions of local similarity between 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.

Sequence similarity searching is one of the more important bioinformatics activities and often provides the first evidence for the function of a newly sequenced gene or piece of sequence. BLAST is probably the most popular similarity search tool. The National Center for Biotechnology Information first introduced BLAST in 1989. The NCBI has continued to maintain and update BLAST since the first version. In 2009, the NCBI introduced a new version of the stand-alone BLAST applications, BLAST+.

The BLAST+ applications have a number of improvements that allow faster searches as well as more flexibility in output formats and in the search input. These improvements include: splitting of longer queries so as to reduce the memory usage and to take advantage of modern CPU architectures; use of a database index to dramatically speed up the search; the ability to save a “search strategy” that can be used later to start a new search; and greater flexibility in the formatting of tabular results.

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