BLAST

BLAST is an acronym for: Basic - Local -Alignment - Search Tool, a bioinformatics tool used to find similarities between biological sequences - usually DNA, RNA or protein sequences. BLAST compares an entered sequence (query) with a database of known sequences to find out:

• whether there are similar (homologous) sequences,
• how strong the similarity is (identity and degree of similarity),
• and where exactly this similarity occurs (alignments).

Typical applications:

• Identification of genes or proteins based on unknown sequences.
• Functional annotation of sequences by comparison with known genes/proteins.
• Phylogenetic analyses (kinship analysis).
• Primer design: avoidance of non-specific binding by comparison with the genome.

Exemplary BLAST variants:

• BLASTn - for nucleotide vs. nucleotide database (e.g. DNA vs. DNA)
• BLASTp - for protein vs. protein database
• BLASTx - translates a DNA sequence into all possible proteins and compares with a protein database
• tBLASTn - compares a protein sequence with a translated nucleotide database
• tBLASTx - compares translated nucleotide sequences at protein level

1. Altschul SF et al.(1990) Basic local alignment search tool. J Mol Biol 215:403-410.