Overview

zDB is designed to perform comparative genomics analyses and to integrate the results in a Django web-application.

Several analyses are currently supported, with more to come:

  • Orthology inference

  • Phylogenetic reconstructions

  • COG annotation

  • KEGG orthologs annotation and pathway completion analysis

  • PFAM domains annotation

  • Virulence factors

  • Antimicrobial resistance genes

  • Swissprot homologs search

  • RefSeq homologs search: implemented, but significantly slows down the analysis. You’ll also have to download and prepare the database for diamond search, as this was not included in the database setup script.

All the results are stored either in a SQLite database or directly as files and displayed in the web application. Interactive visualizations facilitates the comparison of gene content and static figure can be downloaded for publication.

Here is an overview of its architecture:

zDB architecture

If you are not setting up your own database, but instead simply want to use the webapplication of an existing installation, you can directly refer to the website tutorial of the documentation.

If you are setting up your own database, you will need to install zDB, setup some reference databases, run the analysis pipeline and finally launch the web server. An overview of the workflow is shown below:

zDB workflow

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