BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box.

BLAT at Kent Informatics


Kent, W.J. 2002. BLAT — The BLAST-Like Alignment Tool. Genome Research 4: 656-664.