New software provides a better understanding of how viruses evolve

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, who 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.

http://www.southampton.ac.uk/~re1u06/software/sl