Welcome to cblaster’s documentation!

cblaster is a tool for identifying co-located hits in BLAST searches against NCBI sequence databases. It leverages the NCBI’s public APIs to facilitate fully remote searches, requiring no setup of local search databases.

If you find cblaster helpful, please cite:

Cameron L.M. Gilchrist, Thomas J. Booth, Bram van Wersch, Liana van Grieken, Marnix H. Medema, Yit-Heng Chooi (2020).
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters.
bioRxiv 2020.11.08.370601; doi: https://doi.org/10.1101/2020.11.08.370601

To view an example of what cblaster can produce, click here.


  • Fully remote searches against public NCBI sequence databases
  • One command to generate local search databases from many genomes
  • Easy to use graphical user interface (GUI)
  • Fully interactive visualisations

Indices and tables