What is CluSeek?

CluSeek is a universal tool that searches for diverse types of gene clusters, making it a valuable resource for researchers across a variety of biological fields. CluSeek searches for homologs of two or more co-localized genes and their neighborhood (gene clusters) in bacterial genomes within the sequencing data of GenBank database. This easy-to-use tool provides a convenient and efficient way to analyze genomic data and retrieve gene clusters that contain user-selected genes.

Research of specialized Metabolites:
Is CluSeek similar to antiSMASH?

Genome mining of biosynthetic gene clusters is the same research area where you would often use antiSMASH or Prism. However, CluSeek operates on a fundamentally different principle and deals with different types of queries. Both antiSMASH and Prism compare a certain amount of sequencing data (typically a sequenced genome) with an internal library of known biosynthetic gene clusters to find similar gene clusters. On the other hand, CluSeek scans all data within the GenBank database and does not rely on pre-existing internal libraries of known gene clusters. CluSeek can search for gene clusters encoding metabolites with a specific structural motif (based on co-localized biosynthetic genes) or function (based on resistance determinants).

Is CluSeek easy to use?

Yes, CluSeek is easy to use. Although the web-based version is still under development, you can already access CluSeek without difficult installation. CluSeek follows a simple download-open-use principle and has a convenient graphical user interface, making it easy to operate even for users with no IT expertise.

Are there any limitations to using CluSeek?

CluSeek has been developed for prokaryotic genomes; however, preliminary testing shows that it can successfully handle also sequencing data from eukaryotes. Currently, CluSeek is fully compatible with Windows, while its adaptation for other platforms is in progress (let us know if it would be relevant to you).

Can I try using CluSeek now?

Yes! We currently have two versions available for download – and older, but more tested stable version (1.0.0) and the current development version (1.3.5).

We recommend trying the development version, as it offers significant improvements to overall usability, although not all features have yet been implemented and tested. If you have previously downloaded version 1.3.4, we recommend getting version 1.3.5, as it fixes a major issue with the protein grouping algorithm. 

We hope to release additional improvements in the coming weeks.

You can send us your feedback or suggestions at

This version includes many new features, but has not been properly tested and is likely to contain a variety of both known and unknown issues. Nevertheless, the new features offered are a major improvement over the previous version, which is why we are making them available here. Currently, only the Windows version is available. Similarly, a full user manual is not available for this version, instead you can try this quick guide

Most notable features compared to 1.0.0::

    • Saving your data
    • Significantly improved gene cluster analysis interface
    • Expanded data export options
    • The usage of Diamond instead of USEARCH for sequence alignment

Changes compared to 1.3.5

      • Fixed issue with „Save“ button not saving data when a new analysis was created
      • Fixed issue with „Save as“ button not changing the active project to the newly created copy


    1. Download CluSeek here and extract the .zip file
    2. Run the x86_redistributables installer*
    3. That’s it. Run CluSeek and start a project.

    As this version uses regular project files, no elaborate folder management is required – just make sure to save before you exit.

* – These are  libraries distributed for free by Microsoft, which are necessary for the running of Diamond, the sequence aligner used by CluSeek. They only need to be installed once. We provide the installer in the download archive for your convenience, but you may also obtain them directly from Microsoft if you wish.

This is an older version of CluSeek lacking many amenities and improvements. It has, however, been tested and should deliver a more consistent user experience.

  1. Create a folder for CluSeek (on your desktop for instance).
  2. Download CluSeek and extract the files from .zip to the folder for CluSeek.
    Note: CluSeek requires USEARCH for aligning amino acid sequences. CluSeek will download USEARCH by itself automatically. Should that fail, you may download it manually here.
  3. Open x86_redistributables file in the CluSeek folder and confirm its installation.
  4. Open CluSeek in the CluSeek folder and you are ready to start!

Note: A data folder is used to store previously downloaded information. A new one is created automatically if a pre-existing one is not detected. If you wish to purge CluSeek’s memory, simply delete the data folder

A detailed user manual (Version 1.0.0) is available here.

Institue of Microbiology

Institute of Microbiology, CAS
Vídeňská 1083, 142 20 Prague 4 - Krč
The Czech Republic


Institute of Microbiology, CAS
Průmyslová 595, 252 50 Vestec
The Czech Republic

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+420 241 062 371

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