DIAMOND (biotechnology)

DIAMOND is a bioinformatics algorithm and software tool for aligning protein sequences and translated DNA sequences, created by German computer scientist Benjamin J. Buchfink starting in late 2012 as a fast alternative to NCBI's BLAST alignment tool. An earlier version of the underlying method, called SASS, won the U.S. Defense Threat Reduction Agency's one million dollar Algorithm Challenge, aimed at a real computational bottleneck in which researchers were spending roughly 800,000 CPU hours on a supercomputer to compare metagenomic sequencing reads against the KEGG database using BLASTX. DIAMOND speeds up this comparison with a seed-and-extend strategy: it finds short exact matches between the query and target sequences, then extends the promising ones into longer gapped alignments, using indexes built over both the query and target sets to get better use of the CPU cache than older tools. After seeding, it filters candidates heuristically and finishes the surviving alignments with a Smith-Waterman extension. By August 2026 the paper describing DIAMOND had been cited more than 20,000 times.