Entigen is collaborating with the South African National Bioinformatics Institute to develop Clusterall, a new group of datasets for its on-line BioNavigator bioinformatics workspace that will show which genes are expressed or turned off under different conditions.
Under the agreement, Entigen (formerly eBioinformatics), is funding a post-doctoral researcher at SANBI and providing hardware and software tools for the project. SANBI will be able to make the organized datasets publicly available as soon as they are complete, but Entigen will have first access to annotate them and provide “clean access” to them via the BioNavigator portal, where they will be available on a pay-per-view basis.
Clusterall will use algorithms to analyze and assemble ESTs, mRNA, and gene sequence data from a number of organisms, including those with condensed genomes, such as maize, and animals with larger genomes. The information will be compiled in a single database, which the company said would greatly reduce the time researchers currently spend building project-specific gene databases on a one-off basis.
“What we are doing is providing a nicely organized set of genes whereas before we just had a set of ESTs,” said SANBI director Winston Hide. “Entigen is going to pick up these resources and place them within their system, [providing] them in the first annotated and accessible format.”
“The result will be an annotated database of genes that’s 10 times smaller than the combined data sources it was derived from, with inaccuracies, redundancies, and non-gene sequence data selectively removed. With the condensed database, researchers can use more rigorous gene analysis algorithms, locate novel gene variants more easily, and work much faster,” said Hide.
Tim Littlejohn, founder and CSO of Entigen, who sits on the board of SANBI, has been discussing this agreement with the institute for about nine months, Hide said.
“He came to me with initial proposal and said, ‘Winston, don’t you want to cluster a large number of available transcriptants? What we’d like to do at Entigen is go through a process of making [this] available under our structure,’” Hide recounted. “This saved me the effort of generating a grant proposal, and the result is now saving time.”
Hide hopes to use the datasets generated from the collaboration in his evolutionary biology research.
Entigen and SANBI are both members of the European Molecular Biology network, and the Clusterall partnership is the first of several anticipated EMBnet bioinformatics development projects.
James Nelson, vice president of marketing at Entigen, said that the company intends to continue funding the work at SANBI on an ongoing basis to ensure a continuing stream of updated information.