TraDIS-VaultAim

To create a web browser for community access and easy visualisation and comparison of hundreds of TraDIS datasets.

Brief project outline

Professor Henderson's research group studies bacteria and their interaction with humans and animals. Their approach to identifying genes encoding essential functions is Transposon-directed insertion-site sequencing (TraDIS), which couples transposon mutagenesis with DNA sequencing to identify essential regions of a bacterial genome. The current TraDIS library has a median distance between mutations of 2 bp and is the densest mutant library described for any organism; this resource positions the Henderson group uniquely within the global community.

Together with the QCIF Facility for Advanced Bioinformatics (QFAB) and UQ’s Genome Innovation Hub (GIH),  the project will develop TraDIS-Vault, a flexible and user-friendly web-based interface ideal for storing and visualizing microbial genome datasets. We will populate this database with our TraDIS datasets. This will be accompanied by a simple interface to allow users to upload their own datasets for analysis and visualisation.

Genomics-based innovative aspect of proposal

TraDIS-Vault will provide a stable public resource that can be used to store, visualise, and compare multiple TraDIS datasets. We propose to expand this to assimilate relevant microbial RNAseq and ChIPseq datasets into the database providing a comprehensive tool for analysing and integrating genetic information.

Broad applicability of the technique

TraDIS-Vault will be a crucial resource for those studying the fundamentals of bacterial viability and biochemistry, infection, vaccine development and antibiotic development. A web based interaction tool for low resolution genetic interactions based on single gene knockouts libraries was published 8 years ago in Cell and has been cited 450 times; this is the “go-to” resource for all teams studying the fundamental biology of E. coli (https://ecoliwiki.org/tools/chemgen/).  TraDIS-Vault will replace this resource with a much higher level of resolution and expand it to integrate additional pathogens and genomic datasets.

At the technical level, TraDIS-Vault will be based on Web Apollo, a platform for genome annotation that is widely adopted by the genomics community. For example, it is one of the platforms that the Australian BioCommons is deploying to support large initiatives such as the Oz Mammals Genomics initiative. The availability of PacBio Sequel II at UQ will dramatically increase the number of draft genomes being assembled. UQ researchers and collaborators in the fields of agriculture, environmental biology, microbiology as well as human and animal health will require a collaborative platform to share, annotate and curate those draft genomes. This project will enable GIH staff to have exposure to this tool.

Developments arising from this project

TraDIS-Vault can be access from the following link https://tradis-vault.qfab.org/apollo/jbrowse/

Project members

Research collaborators

Professor Ian Henderson

Professor Ian Henderson

Director
Institute for Molecular Bioscience
Affiliate Professor
UQ Centre for Clinical Research, Faculty of Medicine
Affiliate Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
Dr Dom Gorse

Dr Dom Gorse

Director, Data Scientist
QCIF Facility for Advanced Bioinformatics
Michael Thang

Michael Thang

Computational Biologist
QCIF Facility for Advanced Bioinformatics
Nick Rhodes

Nick Rhodes

Database and Systems Administrator
QCIF Facility for Advanced Bioinformatics

Genome Innovation Hub

Valentine Murigneux

Valentine Murigneux

Senior research assistant
Genome Innovation Hub
Bioinformatician
QCIF Facility for Advanced Bioinformatics