BLAT is a bioinformatics software 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. (Source: Kent, W.J. 2002. BLAT --
The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
http://dx.doi.org/10.1101/gr.229202)

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.

WWW: http://users.soe.ucsc.edu/~kent/