May 26, 2018

Fast tool for local sequence similarity searches

BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. Source Kent, W.J. 2002. BLAT – The BLAST-Like Alignment Tool. Genome Research 4 656-664. http//

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome but not the genome itself in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box.

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