BLAST
Bioinformatics · Molecular Biology · Genomics
Say it: BLAST
Short for Basic Local Alignment Search Tool
BLAST is a widely used program that searches databases for DNA or protein sequences similar to a query and ranks the matches by statistical significance.
Also: blastn, blastp
Definition
What is BLAST?
BLAST is a search engine for sequences. You give it a query, such as a gene or protein sequence, and it scans very large databases for regions of local similarity, then lists the best matches with their alignments. It was published in 1990 by Stephen Altschul and colleagues at the US National Center for Biotechnology Information, which still runs the best-known service; the European Bioinformatics Institute offers it too.
Comparing a query with every database entry by exact alignment would be slow, so BLAST takes a shortcut. It splits the query into short words, finds database sequences that share those words, and extends each hit in both directions for as long as the score keeps up. This makes it fast but approximate. Each match comes with a bit score and an E-value, the number of equally good matches expected by chance in a database of that size; the smaller the E-value, the less likely the match is a coincidence.
Different versions compare DNA with DNA, protein with protein, or translate DNA into protein first. Students use BLAST to identify an unknown sequence, find related genes in other species and check that PCR primers are specific.
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Terms that go with it
- Sequence alignmentSequence alignment is a way of lining up two or more DNA, RNA or protein sequences so that matching positions share a column, showing how similar they are.
- FASTA formatFASTA format is a plain-text format for DNA, RNA or protein sequences in which each record starts with a header line beginning with > followed by the sequence.
- BioinformaticsBioinformatics is the science of using computers to gather, store, analyze and share biological data, especially DNA, RNA and protein sequences.
- GenomeA genome is the complete set of DNA in an organism or cell, including all of its genes and the stretches of DNA between them.
- ProteinA protein is a large molecule made of one or more chains of amino acids, folded into a specific shape that determines its job in the body.
- Polymerase chain reactionThe polymerase chain reaction (PCR) is a lab technique that copies one chosen stretch of DNA over and over until there are billions of copies.
Sources
Checked against
Written for biofideX in plain words, after checking these references:
- EMBL-EBI Training: BLAST search
- NCBI BLAST tutorial: The Statistics of Sequence Similarity Scores
- NCBI BLAST Help: References
- Zhang et al. (2024), The Historical Evolution and Significance of Multiple Sequence Alignment, Biomolecules
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