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Bioinformatics update
After identifying a gene involved in a key aspect of tomato and potato quality applications can help to identify the role of the gene in question by comparing it with other genes of known function. A web application developed by EU-SOL partner allows researchers to access the underlying gene databases to ensure they always have the most up to date information at their finger tips.
One important part of the EUSOL project is the characterization of tomato and potato genes. After the DNA sequence of a gene is determined (through the tomato and potato genome projects) bioinformatics tools can be used to find out more about the function of these genes without doing experiments in the lab.
As all organisms evolved from a common ancestor in their past they contain varying amounts of similar genes. Several bioinformatics computer programs search massive databases for genes in other organisms with a similar sequence to the one they are interested in. If a gene with a similar sequence is found whose function has already been worked out, it can help to identify the role of the gene in question. Unfortunately all programs have their own strengths and weaknesses and because of that, a combination of tools is necessary to both check functions assigned by one tool and to assign a function to as many genes as possible.
AFAWE is a web application developed by MPIZ which runs all these programs in parallel on several computers around the world, collects the results of each and shows them in a user friendly web interface. Filters help to distinguish between trustworthy results and non-trustworthy results from each application. Furthermore each user of AFAWE has the possibility to give his or her personal opinion about the function of each gene by adding a “manual curation” to the gene.
There are other applications that run different tools in parallel but none use web services. The advantage of this is that AFAWE is connected to the underlying databases, which maybe stored around the world, and so can access the very latest data.
To read the paper in full please click on this link: Protein function prediction and annotation in an integrated environment powered by web services (AFAWE).
