Sequence search · Software
DIAMOND
Accelerated sequence aligner for comparing protein and translated DNA sequences against protein databases.
What DIAMOND is
DIAMOND is a high-performance sequence aligner designed for large-scale analysis of protein and translated DNA sequences.
The tool was created by Dr Benjamin J. Buchfink, with development spanning the University of Tübingen, the Max Planck Institute for Biology Tübingen, and ongoing support from the Max Planck Society for the Advancement of Science and the German Federal Ministry for Economic Affairs and Energy.
In addition to pairwise alignment, DIAMOND provides protein sequence clustering, frameshift-tolerant alignment for long sequencing reads, and taxonomic classification. It is engineered with low resource overhead, enabling researchers to run large searches on standard desktop and laptop computers as well as high-performance compute clusters.
How it works
DIAMOND performs local pairwise sequence alignments by searching protein and translated DNA sequences against target protein databases. It incorporates frameshift alignment algorithms tailored for long sequencing reads and supports taxonomic classification workflows.
For sequence clustering, DIAMOND DeepClust provides high sensitivity with linear-time scaling, distributing compute workloads across multiple nodes in parallel computing environments.
Key facts
- Version
- 2.1.12
- Category
- Sequence search
- Query inputs
- Protein and translated DNA sequences
- Reference target
- Protein databases
- Alignment speed
- 100x to 10,000x the speed of BLAST
- Supported output formats
- BLAST pairwise, tabular, XML, and taxonomic classification
- Hardware targets
- Standard desktops, laptops, and multi-node compute clusters
What you can use it for
- Translated DNA search
- Searching translated DNA sequences directly against protein reference datasets to detect homologous proteins.
- Long-read frameshift alignment
- Analysing long sequencing reads using frameshift-aware alignment against protein databases.
- Protein sequence clustering
- Grouping vast protein datasets into clusters with linear-time scaling across single machines or parallel multi-node environments.
- Taxonomic classification
- Classifying sequence data taxonomically as part of the alignment workflow.
Run it here
DIAMOND is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
Try asking
“Align these predicted proteins to my reference set with DIAMOND.”
Strengths and limits
Good at
- Clusters protein sequences with high sensitivity, linear-time scaling, and multi-node parallelisation.
- Supports frameshift alignments designed for long read analysis.
- Operates with low resource requirements on standard personal computers as well as multi-node clusters.
- Provides output in BLAST pairwise, tabular, and XML formats alongside taxonomic classifications.
Questions
Can I run DIAMOND online without installing it?
DIAMOND is preinstalled on the machine behind every research conversation. Ask the agent in plain language, or give it the exact command — it runs it, reads the output and explains it.
What licence is DIAMOND under?
DIAMOND is published under its authors' own licence; the project page at https://github.com/bbuchfink/diamond states it.
What sequence types does DIAMOND align?
DIAMOND aligns protein and translated DNA query sequences against protein reference databases.
What hardware is required to run DIAMOND?
It is designed with low resource requirements and runs on standard laptops and desktops, while also scaling across multi-node compute clusters.
Does DIAMOND support long sequencing reads?
Yes, it includes frameshift alignment capabilities specifically intended for long read analysis.
Which output formats can DIAMOND generate?
It can output alignments in BLAST pairwise, tabular, and XML formats, as well as taxonomic classification results.
How to cite it
Buchfink BJ, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18, 366–368 (2021). doi:10.1038/s41592-021-01101-x
Written from DIAMOND's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.