blast

BLAST, or Basic Local Alignment Search Tool, is a bioinformatics program used to compare nucleotide or protein sequences against sequence databases to identify homologs and infer function. Developed in the 1990s at the National Center for Biotechnology Information (NCBI) and collaborating groups, BLAST provides fast, heuristic sequence similarity searching that balances sensitivity and speed, making it a standard tool in genomics and molecular biology.

BLAST locates short seed matches between a query and database sequences and extends them to higher-scoring alignments. It uses scoring matrices such as BLOSUM or PAM and can generate gapped alignments in later variants. Significance is reported with E-values, based on Karlin-Altschul statistics, allowing users to assess matches in the context of database size.

Variants include BLASTN (nucleotide-nucleotide), BLASTP (protein-protein), BLASTX (translated nucleotide query against a protein database), TBLASTN (protein query against a translated nucleotide database), and TBLASTX (translated nucleotide against translated nucleotide). PSI-BLAST builds a position-specific scoring matrix iteratively, while DELTA-BLAST uses conserved domains to boost sensitivity. Outputs typically include lists of hits, alignments, scores, and E-values, aiding functional annotation and comparative genomics.

Since its introduction, BLAST has become a staple of sequence analysis, widely used in genome annotation, evolutionary studies, and metagenomics. While fast and generally reliable, it is less sensitive than exhaustive methods for very distantly related or short sequences and depends on database quality and parameter choices. It has spurred the development of many successors but remains foundational in bioinformatics.