BLAT vs BLAST

http://genome.ucsc.edu/FAQ/FAQblat.html

From a practical standpoint, Blat has several advantages over BLAST:

* speed (no queues, response in seconds) at the price of lesser homology depth
* the ability to submit a long list of simultaneous queries in fasta format
* five convenient output sort options
* a direct link into the UCSC browser
* alignment block details in natural genomic order
* an option to launch the alignment later as part of a custom track

Blat is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA,

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats. The index takes up a bit less than a gigabyte of RAM. The genome itself is not kept in memory, allowing BLAT to deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes.

BLAT was written by Jim Kent. Like most of Jim's software, interactive use on this web server is free to all. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. See the Kent Informatics website for details.