Fast and sensitive protein alignment using DIAMOND
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Updated: Apr 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Benjamin Buchfink1, Chao Xie2, Daniel H Huson3
1Department of Computer Science and Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
Abstract:
The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.

