Nucleic Acids Research, 2001, Vol. 29, No. 1 66-69
© 2001 Oxford University Press
PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data
Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104-6018, USA
The Plasmodium falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1–14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.
* Correspondence should be addressed to: David S. Roos, Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104-6018, USA. Tel: +1 215 898 2118; Fax: +1 215 898 8780; Email: droos@sas.upenn.edu Current members of the Plasmodium Genome Database Collaborative include: J. C. Kissinger, A. J. Milgram, M. J. Fraunholz, and D. S. Roos (Department of Biology, University of Pennsylvania); B. P. Brunk, J. Crabtree, S. J. Diskin, J. Schug, G. C. Overton, and C. J. Stoeckert Jr (Center for Bioinformatics, University of Pennsylvania); R. L. Coppel and R. L. Huestis (Deparment of Microbiology, Momash University).
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