New success for University of South Wales researchers

July 31, 2013

Researchers at the University of South Wales have made an important contribution to the field of genomics with the publication of a new paper* on gene analysis in one of the most highly regarded journals in the field.

Researchers at the University of South Wales have made an important contribution to the field of genomics with the publication of a new paper* on gene analysis in one of the most highly regarded journals in the field.

Almost every week it is reported that another biological species has had its DNA sequenced and this technology has the potential to revolutionise fields such as medicine and agriculture.

However, one of the major limitations delaying the exploitation of modern genomic technology is the difficulty in analysing the huge amounts of data that are produced.

These datasets consist of many terabytes (trillion bytes) of DNA sequences that need to be ordered and analysed so that researchers can find the genes and the genetic switches that control their expression. This laborious process has been described as looking for a very small needle in an extremely large haystack.

The University of South Wales team – Professor Denis Murphy, Dr Tatiana Tatarinova and Martin Triska – have now developed a novel genome analysis tool that will greatly assist researchers in the future.

Their success is largely thanks to access to the facilities of the High Performance Computing (HPC) Wales network and the expertise of computing staff Dravid Grocutt and James Southern, at the Fujitsu Laboratories of Europe, which together with the Welsh Government helps to fund HPC Wales as one of the most powerful computational tools in Europe.

The new genomics tool, CisExpress, is specially designed for use with very large datasets. The tool facilitates the identification of regulatory motifs in genes and gives very valuable information about potential molecular mechanisms of co-regulation of genes in different conditions.

David Craddock, CEO of HPC Wales said: “HPC Wales is delighted to have supported the University of South Wales in making the CisExpress tool available to bioinformaticians all over the world. This marks an exciting step forward in the field of genomics and we are delighted that our technology has powered this research. Supercomputing technology provides academic researchers with the ability to analyse vast amounts of data more quickly than has ever been possible previously, and it is a privilege to be able to support research that will have a potentially revolutionary impact.”

CisExpress is potentially applicable for use with a wide range of genomic databases for any species of interest – from humans to wheat. While CisExpress is designed as a publicly available tool, the University of South Wales research team is also planning to develop new commercial genomic tools in collaboration with international partners and a new Welsh startup company based near Pontypridd.

  • Triska et al (2013) CisExpress: Motif detection in DNA sequences, Bioinformatics, doi 10.1093/bioinformatics/btt366

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