CluSeek

ClusterSeeker
Download CluSeek

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?

Please note that the current version of CluSeek remains a work in progress and not all features are fully functional. 

Installation:

  1. Download CluSeek here and extract the .zip file
  2. If you are installing CluSeek on your computer for the first time, you will need to install the Windows redistributables (vc_redist.x86) included with CluSeek, or download and install the latest version from microsoft.
  3. That’s it. Run CluSeek and start a project.

We hope to release additional improvements in the coming weeks.

You can send us your feedback or suggestions at cluseek@biomed.cas.cz

Try the development version (1.4.11)

This version includes many new features, but please note that the current version of CluSeek remains a work in progress and not all features are fully functional. Notably, in this version, exporting a specific highlighted region is not possible and may result in a crash.

Download CluSeek here and extract the .zip file

Try the development version (1.3.6)

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. 

Download CluSeek (1.3.6) here 

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 
    • 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 

Try the development version (1.0.0)

This is an first public version of CluSeek.

  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

BIOCEV

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

Contact Us

lab111@biomed.cas.cz
+420 241 062 371

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