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BLAT is the Blast-Like Alignment Tool.

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BLAT is quite similar to the sequence searching tool BLAST in that it quickly searches for short sequence matches and then extends those into high-scoring pairs. Whereas BLAST will index the query sequence and scan linearly through the reference sequence (also called the 'database sequence',) BLAT indexes the reference sequence and scans linearly through the query. The index is not large and can be held in the memory of a standard desktop computer. This increases the speed significantly. [1]



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  1. Kent, WJ (2002) BLAT--the BLAST-like alignment tool. Genome Res. 12 656-64 PubMed