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Basic Information

Author Stephen Altschul, Warren Gish, David Lipman
Year 1990
Reference Basic local alignment search tool
Short description Alignment Heuristic
Method seed words

BLAST, Basic Local Alignment Search Tool, 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 is a heuristic to the calculation of optimal alignments calculated by dynamic programming.


In a first step BLAST locates short words, with significant scores and a certain length (e.g. 3) within a sequence, this is called seeding. These first matches are used for local alignments. High scoring words within a database can be pre-calculated. The challenge of BLAST was to calculate proper statistics for the searches.