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Bioinformatics: ND's Collins parlays mosquito work into new NIAID center

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Frank Collins has been studying the mosquito Anopheles gambiae for nearly 25 years, ever since he stumbled across an unused colony of the insects in the corner of the NIH lab he did his postdoc in. When genomics began to touch the world of the mosquito, Collins, now director of the Center for Tropical Disease Research and Training at the University of Notre Dame, jumped right in.

About four years ago, Collins and his colleagues proposed a preliminary genome project on Anopheles, a vector of malaria, and won funding through NIAID. The goal was not to do a full-blown genome project but to set the stage for one: Collins worked on sequencing a selection of ESTs and physical mapping of many BACs, among other things. As luck would have it, while he was engrossed in that project, Celera Genomics successfully applied to NIAID for funding to do a shotgun sequence of Anopheles. “We had to have some way of displaying this genome,” Collins says, “so we used some of the funds [to] get an Ensembl-based display of the Anopheles genome through EBI.” Today, he adds, that remains the primary portal scientists use to browse the mosquito’s genome.

That work proved to be the launching pad for what would wind up to be a five-year, $10 million contract from NIAID to be the lead among seven organizations in developing a publicly available bioinformatics tool and resource center called VectorBase. VectorBase will be a genome browser (what Collins calls a “genome information management system”) specifically adapted to the genomes of arthropods known to transmit pathogens, he says. “You need more than GenBank for these [organisms].” Notre Dame’s component includes responsibility for producing an EST database and a population genetics database, as well as tools for comparing and displaying data and building a Web interface.

The main goal for VectorBase is “an easily accessed system for managing, analyzing, and displaying the draft genomes that are becoming available,” Collins says. He envisions adding plenty of tools to the program — particularly ones to help scientists look at variation and other population phenomena within a species — though he says many of those tools will likely remain undefined until the program has been used enough to see what’s missing. “In three, four, five years it will probably do a lot of things that we don’t foresee right now,” he says.

That’s also due in part to the limited availability of draft arthropod genomes right now. “When we wrote this proposal, we realized there was really only one draft genome available, but there were a number of others coming along,” Collins says. “The contract was set up by NIAID to be a contract for managing at least five different genomes.”

— Meredith Salisbury

 

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