Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. BLAT (the BLAST-Like Alignment Tool) is a software program developed by Jim Kent at UCSC to identify similarities between DNA sequences and protein sequences. It was developed to assist in the annotation of the human genome sequence. BLAT's license makes it free for non-commercial use.[1]
BLAT is much faster than older tools such as BLAST for nucleotide and protein alignments, and it can also perform spliced alignments of RNA to DNA.
BLAT uses a space-time tradeoff to compare sequences quickly. BLAT precomputes an index of all nonoverlapping k-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be similar to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible.[2][3]