User Guide

The cblaster software was written by Cameron Gilchrist with contributions from Dr. Thomas Booth and Dr. Yit-Heng Chooi.

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

If you have any questions, would like to report a bug, or have any suggestion on how we could improve cblaster, please contact:

• cameron.gilchrist@research.uwa.edu.au
• thomas.booth@uwa.edu.au
• yitheng.chooi@uwa.edu.au

Table of Contents

• What is cblaster
• Installation and Quick Start
  • Installing Python for Windows
  • Installing DIAMOND
  • Installing, uninstalling and updating cblaster
  • Running your first search
• Pre-search configuration using the config module
• Running a cblaster search using the search module
  • The cblaster search workflow
  • Searches against local sequence data
  • Functional domain searches using HMMER
  • Remote searches against NCBI sequence databases
  • Specifying filters
  • Specifying output
  • Saving search sessions and recomputing outputs
  • Finding intermediate genes between hits
• Creating local sequence databases with the makedb module
• Estimating genomic neighbourhood with the gne module
• Retrieving hit sequences with the extract module
• Extracting GenBank files from session files using extract_clusters
  • Example usage
• Plotting extracted clusters using plot_clusters
  • Example usage
• Using the graphical user interface (GUI)
• Miscellaneous functions
  • Accessing help dialogues
  • JSON indent level