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.





  • Bridges


To see what other modules are needed, what commands are available and how to get additional help type

module help blat


To see what versions of BLAT are available type

module avail blat


To run BLAT, include a command like this in your batch script to load the BLAT module:

module load  blat

User Information

Connect to PSC systems:
Technical questions:

Send mail to or call the PSC hotline: 412-268-6350.