14 DAY TRIAL // Understanding the evolution of dangerous viral strains is of paramount importance in microbiology, because it offers a better view of how some of the modern-day types, such as the swine flu virus (influenza type A H1N1), came to be from older strains. That is why investigators at the University of Southampton's School of Electronics and Computer Science-based organization OMII-UK, and the university's School of Biological Sciences pooled their resources together, and used the most advanced computing power at the institution to create the new software, which is able to shed light on viral evolution, AlphaGalileo reports.
With the help of the latest e-Research techniques, and the SLiMFinder program, the experts were able to better understand the similarities and differences that existed between comparable types of proteins in viruses and in humans. The target of the investigation was analyzing short, linear motifs generated by interacting proteins, known as SLiMs. In charge of the effort was the Head of the Bioinformatics and Molecular Evolution Group at US, Dr. Richard Edwards.
“A protein can be thought of as a sequence of amino acids, like beads on a string. SLiMs consist of about three-to-five specific amino acids in the protein and could be responsible for the signaling 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 signaling pathway controlled by the SLiM,” Edwards explains.
“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,” the expert adds. The main idea behind SLiMFinder was to enable it to make use of a very complex and accurate workflow, which basically refers to the automation of repetitive tasks. These tasks include peering through databases and collecting data from them, as well as allowing for the manipulation of these pieces of information via a user-friendly interface.