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BLAT is a tool from Jim Kent's stable at UCSD. In purpose it is very close to NCBI's BLAST, but it generally is easier in terms of switches and input options.


module load blat

to load up the module.

Typical usage would be to, given a reference sequence for a gene, to look for that gene sequence in a different reference.

blat <db.fa> <query> out.psl


  • There are no mandatory switches (there are optional ones though, for example --ooc for an external 11-mer file)
  • the database FASTA does not need indexing, and it comes first in the list of arguments. Databse often abbreviated to T for target.
  • the query is second, query often abbreviated to Q.
  • the ouput file is in its own format, called PSL, but is easily read in a text editor.