BLAT 3.5

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome.

Blat produces two major classes of alignments:

  • at the DNA level between two sequences that are of 95% or greater identity, but which may include   large inserts.
  • at the protein or translated DNA level between sequences that are of 80% or greater identity and   may also include large inserts.

Accessing the software

To load the module:

$ module load BLAT/3.5-iomkl-2018a

Command-line options can be viewed by issuing the following command with the module loaded:

$ blat

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the BLAT website for more information regarding this application.

Last modified: 25 June 2018