BLAST is a widely used tool for finding biological sequences that resemble a sequence of interest. This lesson introduces its purpose, history, basic inputs, and typical output.
BLAST stands for Basic Local Alignment Search Tool. It is an algorithm and software program for comparing primary biological sequences, including protein amino-acid sequences and DNA or RNA nucleotide sequences. A sequence supplied for searching is called the query; the sequences searched against are the database or target.
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What is BLAST?
BLAST, or Basic Local Alignment Search Tool, is an algorithm and program that finds local similarities between a biological query sequence and sequences in a target database.
What is a query sequence?
It is the sequence supplied by the researcher as the sequence of interest. BLAST compares it with a target sequence or database.
Why does BLAST use a heuristic method?
A heuristic method reduces the search effort, making sequence comparison practical for very large databases. Its speed comes with the possibility of missing some matches.
How does Smith–Waterman differ from BLAST?
Smith–Waterman finds an optimal local alignment for a sequence pair but is generally slower and more resource-intensive. BLAST searches heuristically for speed and does not guarantee an optimal result.
What information can a BLAST result contain?
It can contain a graphical overview of hits, a table of matched sequence identifiers and scores, and alignments showing corresponding regions of the query and database sequences.
Quiz questions
Which query and target pairing describes BLASTx?Answer: A nucleotide query translated in six frames and searched against a protein database.
What does a BLAST E-value estimate?Answer: The expected number of chance alignments scoring at least as highly in the database search.
Which filter is used for low-complexity regions in DNA sequences?Answer: DUST
What is a high-scoring segment pair (HSP) in BLAST?Answer: A local alignment region with a score high relative to the scoring system.
How does database segmentation support parallel BLAST searches?Answer: Processors search separate database parts, and their results are merged.