prokaryotes

Prokaryotes bioinformatics

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Bioinformatics is of increasing importance in order to enable the timely evaluation of potential threat that new strains for example may pose to food safety and biosecurity by rapidly delivering a complete genome, finished genome sequence. This can only be achieved when the right processes and data access arrangements to support the bioinformatics required for annotating the genome are in place.

Such a process involves looking at the genomic sequence, working out where the genes themselves are and what they might do. This is done by comparison with genes of known function (for example, from other bacteria). Similarly for disease control, bioinformatics is being used to adapt miniaturised sequencing device to conduct live environmental surveillance, which enables researchers to deliver real-­‐time experimental genetic data for immediate analysis. Such bioinformatics applications can also be used to develop sensing system by sequencing environmental samples, containing DNA from hundreds or thousands of different organisms.

The ability to set up a tool box and adequate resources for accessibility, storage and exploration of procaryotes information relies on a robust bioinformatics infrastructure. This needs to be portable, interoperable and when it comes to data, adopt the FAIR principles to  create a sustainable and scalable environment for the exploration of ‘omics data for a particular organisms of interest as well as across different types of data and species.

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An adaptable bioinformatics framework for Prokaryotes

The role that bioinformatics and modern DNA sequencing techniques play in all aspects of microbiology continues to grow; influencing the reach and scale of work in this field. In the news we are seeing the direct benefit of the application bioinformatics and sequencing to the control of disease (eg. ebola) and a greater ability to understand complex microbial communities (e.g the Human Microbiome Project). The EMBL-ABR: Melbourne Bioinformatics Node is playing a significant role in transforming the fundamental approach to public health microbiology – enabling a transition from traditional laboratory based typing of bacterial isolates arriving at the Microbiological Diagnostic Unit Public Health Laboratory (MDUPHL) to a situation in the not too distant future where the basis for typing of an isolate will be its genome sequence. EMBL-ABR: Melbourne Bioinformatics Node has had a significant role in establishing the bioinformatics methods to enable the efficient collection, storage, analysis and publication of these genomic data.

Our expertise in microbial bioinformatics provides us with the capability to contribute to the development of analysis methods for the new applications of not only current but evolving DNA sequencing techniques eg. we are involved in projects that are developing methods for whole genome shotgun sequencing of clinical specimens.

The EMBL-ABR has a significant role in the future of increasingly big data driven fields such as microbiology. Through existing projects we have brokered access to national computing infrastructure, provided access and training on the Genomics Virtual Laboratory (EMBL-ABR: Melbourne Bioinformatics Node is part of the team developing this ‘life-scientist friendly’ analysis platform) and enabled access to a range of large, publicly-available, data sets.

EMBL-ABR Activity Lead: Prokaryotes
Dieter

Dieter Bulach is the EMBL-ABR Activity Lead for Prokaryotes Bioinformatics. Dieter is part of EMBL-ABR: Melbourne Bioinformatics Node. Dieter is specialised in microbiology and bioinformatics and is involved in several projects dealing with viruses and bacteria, specially pathogens. To get involved in this activity or to find out more, please get in touch with Dieter.