Chapter 8. BLAT

BLAT (BLAST-Like Alignment Tool) is a very fast sequence alignment tool similar to BLAST. It's relatively new compared to BLAST, but is becoming very popular. We like it a lot. BLAT is more accurate and can be hundreds of times faster than BLAST. BLAT's speed comes from its runtime indexing of all nonoverlapping subsequences of given lengths. This index is small enough to fit into computer memory and is typically computed only once for each genome assembly. Jim Kent developed BLAT specifically to help with genome assembly while working on the human genome. For details see Section 8.2 at the end of this chapter. We're using Version 16 of BLAT.

An example of a BLAT command-line entry:

blat database query [-ooc=11.ooc] output.psl

where:

• database is a .fa file, a .nib file, or a list of .fa or .nib files.

• query is a .fa, .nib, or list of .fa or .nib files.

• -ooc=11.ooc tells the program to load over-occurring 11-mers from an external file. This will increase the speed by a factor of 40 in many cases, but is not required.

• output.psl is where to put the output.