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In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library 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. The BLAST program was designed by Eugene Myers, Stephen Altschul, Warren Gish, David J. Lipman and Webb Miller at the NIH and was published in J. Mol. Biol. in 1990.
Additional recommended knowledge
BLAST is one of the most widely used bioinformatics programs, because it addresses a fundamental problem and the algorithm emphasizes speed over sensitivity. 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.
Examples of other questions that researchers use BLAST to answer are
BLAST is also often used as part of other algorithms that require approximate sequence matching.
The BLAST algorithm and the computer program that implements it were developed by Stephen Altschul, Warren Gish, David Lipman at the U.S. National Center for Biotechnology Information (NCBI), Webb Miller at The Pennsylvania State University, and Gene Myers at the University of Arizona. It is available on the web at . Alternative implementations are available at  (WU-BLAST) and  (FSA-BLAST).
Input and Output, complies to the FASTA format
To run, BLAST requires two sequences as input: a query sequence (also called the target sequence) and a sequence database. BLAST will find subsequences in the query that are similar to subsequences in the database. In typical usage, the query sequence is much smaller than the database, e.g., the query may be one thousand nucleotides while the database is several billion nucleotides.
BLAST searches for high scoring sequence alignments between the query sequence and sequences in the database using a heuristic approach that approximates the Smith-Waterman algorithm. The exhaustive Smith-Waterman approach is too slow for searching large genomic databases such as GenBank. Therefore, the BLAST algorithm uses a heuristic approach that is slightly less accurate than Smith-Waterman but over 50 times faster. The speed and relatively good accuracy of BLAST are the key technical innovation of the BLAST programs and arguably why the tool is the most popular bioinformatics search tool.
The BLAST algorithm can be conceptually divided into three stages.
..AGTTAC.. | ||| ..ACTTAG..
If a high-scoring un-gapped alignment is found, the database sequence is passed on to the third stage.
An extremely fast but considerably less sensitive alternative to BLAST that compares nucleotide sequences to the genome is BLAT (Blast Like Alignment Tool). A version designed for comparing multiple large genomes or chromosomes is BLASTZ.
Parallel BLAST versions are implemented using MPI, Pthreads and are ported on various platforms including Windows, Linux, Solaris, OSX, and AIX. Popular approaches to parallelize BLAST include query distribution, hash table segmentation, computation parallelization, and database segmentation(partition).
The BLAST program can either be downloaded and run as a command-line utility "blastall" or accessed for free over the web. The BLAST web server, hosted by the NCBI, allows anyone with a web browser to perform similarity searches against constantly updated databases of proteins and DNA that include most of the newly sequenced organisms.
BLAST is actually a family of programs (all included in the blastall executable). The following are some of the programs, ranked mostly in order of importance:
|Databases supported by Bioinformatic Harvester|
|NCBI-BLAST | CDD | Ensembl | Entrez | Flybase | Flymine | GFP-cDNA | Genome_browser | GeneCard | Google_Scholar | GoPubMed | HomoloGene | iHOP | IPI | OMIM | Mitocheck | PSORT | PolyMeta | UniProt | SOURCE | SOSUI | RZPD | Sciencenet | STRING | SMART | ZFIN ||