Researchers at the University of Pennsylvania have developed a new version of the PlasmoDB database, a repository for the sequence of Plasmodium falciparum, a common malarial pathogen, that allows bench researchers without experience in computational biology to directly query unfinished sequence information.
The database, available at http://PlasmoDB.org, contains raw and partially annotated sequence data collected from The Institute for Genomics Research, the Naval Medical Research Center, the Stanford Genome Technology Center, and the Sanger Center, and adds a graphical interface through which researchers can apply several bioinformatics tools for gene prediction and similarity-based searches.
The bioinformatics tools built into the database are not unique and many are publicly available, said David Roos, a biologist at Penn who helped coordinate the database development, but the approach is unusual because it makes these tools easily accessible to biologists, he said.
“The philosophy that motivates the database is not so much to provide researchers with finished, annotated data, but [to provide] tools that enable them to ask their own questions,” said Roos, who also directs the Penn Genome Institute.
The Plasmo-DB-GUS allows users to search a relational database simultaneously for predicted intron/exon structure, chromosome position, Blast similarities, and other criteria. Other capabilities of the database include text-based queries and tools for downloading sequence data in multiple formats. PlasmoDB is also available in a CD-ROM.
Malaria researchers expressed enthusiasm for the PlasmoDB project as a useful resource and good model for providing bioinformatics tools to research scientists not well versed in writing code.
“Having a central place where all data on the Plasmodium genome and related topics is collated is extremely valuable to the field,” said Dyann Wirth, the director of the Harvard Malaria Initiative, who plans to include her group’s recently completed transcriptional profiling analysis of the Plasmodium genome in the database.
It’s actually very useful,” added Chuong Huynh, a database manager and coordinator at the National Center for Biotechnology Information. “In the past, it’s been hard for people to do these kinds of analyses.”
The only worry, said Huynh, is that providing laboratory researchers with such easy access to bioinformatics tools may preclude biologists gaining an understanding of what the tools may be doing. “If you make it too easy, people might not know what is happening inside the black box.” But he added that “in any case the malaria community definitely finds it very useful.”