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Nucleic Acids Research, 2003, Vol. 31, No. 1 212-215
© 2003 Oxford University Press

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

Amit Bahl, Brian Brunk1, Jonathan Crabtree1, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant1, Hagai Ginsburg2, Dinesh Gupta3, Jessica C. Kissinger4, Philip Labo, Li Li, Matthew D. Mailman1, Arthur J. Milgram, David S. Pearson5, David S. Roos*, Jonathan Schug1, Christian J. Stoeckert, Jr1 and Patricia Whetzel1

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA 1 Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA 2 Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel 3 International Center for Genetic Engineering and Biotechnology, Delhi 110067, India 4 Department of Genetics, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA 5 BBN, 10 Moulton Street, Cambridge, MA 02138, USA

*To whom correspondence should be addressed. Tel: +1 2158982118; Fax: +1 2157466697; Email: droos{at}sas.upenn.edu

ABSTRACT

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org).


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