New software to understand viruses

Computer scientists and biologists at the University of Southampton have used the combined power of computing resources within the institution to develop software which provides a better understanding of how viruses evolve.

Researchers from OMII-UK, an organisation based at the University's School of Electronics and Computer Science, and a team from the School of Biological Sciences worked together to try and better understand viruses using the latest e-Research techniques.

Dr Richard Edwards, head of the Bioinformatics and Molecular Evolution Group at the School of Biological Sciences, studies how proteins interact and is particularly interested in short, linear motifs, known as SLiMs, worked with OMII-UK to extend his successful software SLiMFinder, a system which compares viral and human proteins and allows biologists to understand both forms better.

“A protein can be thought of as a sequence of amino acids, like beads on a string,” explains Dr Edwards. “SLiMs consist of about three-to-five specific amino acids in the protein and could be responsible for the signalling pathways between many proteins, because they control the ways in which proteins interact. They are potentially useful to viruses too. They are small so it is relatively easy for a virus to evolve a structure that mimics them, and hijack the signalling pathway controlled by the SLiM.”

As a result of his studies, Dr Edwards wrote SLiMFinder which predicts the SLiMs responsible for specific protein interactions (including those used by viruses to manipulate their hosts).

This collaboration focused on the creation of a workflow for SLiMFinder, which used OMII-UK’s very successful Taverna software. This allows the automation of repetitive tasks, such as data collection from databases, or data manipulation, and provides a user-friendly interface. Development of the software was funded by the Engage project, which brings together the software expertise of OMII-UK and the infrastructure of the National Grid Service to help researchers around the country adopt e-Research techniques.

“This superior ease of use, combined with faster execution times, is helping to make SLiMFinder into a tool that could be of great interest throughout biological sciences,” said Dr Edwards.

Further information

Further information about SLiMFinder can be found at: https://www.southampton.ac.uk/~re1u06/software/slimfinder/ and in the peer-reviewed paper: Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2(10): e967, which can be viewed at: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000967 .

Dr Richard Edwards is head of the Bioinformatics and Molecular Evolution group at the University of Southampton. The University’s School of Biological Sciences specialises in multidisciplinary ‘bench to bedside’ research into conditions such as cancers, heart disease and neuroscience, as well as plant biology and ecology. It is set to move to a state-of-the-art Life Sciences building on the Highfield Campus in 2010. For more information about Dr Edwards, please visit www.sbs.soton.ac.uk/staff/rje/rje.php .

OMII-UK's mission is to cultivate and sustain community software important to research. We are an open-source organisation which provides free software for use in all disciplines of research. OMII-UK is a collaboration between three world-class research sites within the UK: the School of Electronics and Computer Science at the University of Southampton, the OGSA-DAI group at the University of Edinburgh and the myGrid group at the University of Manchester. For information about OMII-UK, please visit http://www.omii.ac.uk/ .