BLAT

BLAT, short for BLAST-like Alignment Tool, is a fast sequence alignment program originally developed by Jim Kent for the UCSC Genome Browser project. It is designed to quickly align a query nucleotide or protein sequence against a large reference genome or against translated genomes, with particular strength for mapping mRNA or cDNA to a genome. BLAT is widely used in gene annotation workflows to identify exon–intron structure and to verify transcripts.

The program uses a seed-and-extend approach. The reference genome is indexed with short exact words (seed sequences, around 11 nucleotides long). When a query contains a matching seed, BLAT examines the surrounding region and extends the alignment to produce high-scoring local alignments, typically reporting the best matches in terms of identity and coverage. It emphasizes speed on large genomes and can operate in DNA-to-DNA or translated protein-to-genome mode. The default output, PSL format, is compatible with the UCSC Genome Browser and can be converted to other formats.

BLAT is not as sensitive as BLAST for detecting distant or divergent homology; it is optimized for high-identity, longer alignments and for rapidly identifying candidate genomic loci for transcripts or genes. It is generally used for mapping mRNA/cDNA to a reference genome, locating exon boundaries, and supporting genome annotation pipelines. BLAT is open-source, implemented in C, and distributed as part of UCSC tools; it can be run locally or embedded in pipelines and supports batch querying against pre-built genome indexes.