BLAT

BLAT (BLAST-Like Alignment Tool) on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates.

BLAT was written by Jim Kent at UCSC.

Documentation

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

Usage on Bridges-2

To see what versions of BLAT are available and if there is more than one, which is the default, along with some help, type

module spider blat

To use BLAT, include a command like this in your batch script or interactive session to load the BLAT module: (note ‘module load’ is case-sensitive):

module load BLAT