BLAT

BLAT (BLAST-Like Alignment Tool) was developed at the UCSC (University of California, Santa Cruz). BLAT uses query sequences to quickly find sequences of 90-95% and greater similarity of length 40 bases or more. BLAT will find perfect sequence matches of 33 bases, and sometimes find them down to 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 12-mers except for those heavily involved in repeats. This index need only be computed once for each genome assembly. Taken together, BLAT can be used to locate extremely fast DNA or protein sequences within the UCSC genome browser. An example of use was the fast alignment of very large human EST datasets onto the human genome. Where BLAST builds an index of the query sequence and the scans linearly through the database, BLAT builds an index of the database and then scans linearly through the query sequence. Where BLAST triggers an extension when one or two hits occur in proximity to each other, BLAT can trigger extensions on any number of perfect or near-perfect hits. Also, a BLAT output can be of great advantage as it shows not only the parts of the genomic sequence matching to a query cDNA sequence but also the sequences in between (introns), which is not shown if you perform a BLAST search at the NCBI ! Thus, BLAT effectively "unsplices" mRNA onto the genome, giving a single
alignment. Thus, BLAT is an extremely effective tool for doing nucleotide alignments between mRNA and genomic DNA
taken from the same species. (http://homepage.univie.ac.at/herbert.mayer/MainSIM.html )