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 exceed 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.