3 May 2010
Jalview drives data quest
A powerful computational tool developed at the University of Dundee is helping drive a modern era of highly complex medical and biological research.
The 'Jalview' software developed within the College of Life Sciences at Dundee makes possible the analysis of vast quantities of data generated by studies of DNA and protein molecules. These are key in fields as varied as crop research, microbial studies, human health and disease studies.
'Medical and biological research is producing enormous quantities of data about the DNA and protein molecules that make up all living organisms and are central to understanding function and disease,' said Professor Geoff Barton, Professor of Bioinformatics in the College of Life Sciences.
'While generating data is getting easier and cheaper, the sheer volume of data arising out of these studies presents big problems for scientists in terms of visualising and analysing what it all means. The Jalview software we have developed makes it easier to carry out common analyses on biological sequences, but most importantly makes possible analyses that would otherwise be too difficult or impossible to do.
'It is effectively a specialised word processor, web-browser and desktop publishing package rolled into one.'
Sequence analysis is central to all modern biological research, whether in agriculture, biotechnology, or the study and treatment of human disease and is used daily by scientists working in all these fields. The Jalview software is installed on over 20,000 computers worldwide and is also available as an applet that is installed on over 100,000 web pages including those run by major international databases.
A key measure of the software’s influence is in the number of citations for it in scientific research, which are running at around 170 per year over the last six years.
The latest updates to the Jalview system have been documented in a research paper by Professor Barton and colleagues which has been described on the influential sciencewatch.com website as the 'Hot New Paper' in the field of computer science.
'The paper describes the latest version of the software and some of the significant updates we have made, including more sophisticated functions and visualisation methods,' said Professor Barton.
'We will be continuing to develop the software to reflect advances made in medical and biological research. Sequences of DNA, RNA, and proteins are the fundamental currency of modern research and things are becoming more advanced all the time.
'As an example, next-generation sequencing technology has become available over the last three years and has led to an explosion in the volume of sequence data available. This volume of data presents significant challenges for visualization and analysis. Already, some protein families have over 100,000 members and this will be the norm for most families of proteins analysed within the next five years.
'Accordingly, we will be developing Jalview to work efficiently with such large sequence families as well as longer sequences such as complete genomes. We will also be making it easier for other scientists to add new features to the program that are specific to their needs.'
The work of Professor Barton and his colleagues at Dundee to develop Jalview has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC).
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