BLAST (Basic Local Alignment Search Tool)

BLAST is one of the most commonly used search tools to perform a protein or nucleotide search of a single query sequence against a database of sequences.  The BLAST algorithm works by finding a short, or local, region of high similarity between two sequences, and then extending this match out from this starting point to both the left and the right.  A score is assigned to the match.  The score will increase as more residues are found to match and will decrease if there are gaps in the alignment.  Alignments with a score that exceeds a certain threshold are reported in the output.

Blastn is the standard nucleotide BLAST search, where a nucleotide query sequence is searched against a nucleotide database.

Blastp searches a protein query sequence against a protein database.

Blastx searches both strands of a nucleotide query sequence against a protein database.  The query sequence is translated into all three reading frames on both strands.

Blast Usage

Blast Databases

Blast Command Line Parameters

Blast Commonly Used Search Parameters

Blast Fasta File Format

Blast Genbank File Format