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PlasmoDB


NAR Molecular Biology Database Collection entry number 91
Bahl, A.1, Brunk, B.2, Coppel, R. L.3, Crabtree, J.2, Diskin, S. J.2, Fraunholz, M. J.1, Grant, G. R.2, Gupta, D.1, Huestis, R. L.3, Kissinger, J. C.1, Labo, P.1, Li, L.1, McWeeney, S. K.2, Milgram, A. J.1, Roos, D. S.1, Schug, J.2, Stoeckert, C. J. Jr.2
1Department of Biology University of Pennsylvania 415 S. University Ave. Philadelphia, PA 19104-6018 USA
2Center for Bioinformatics University of Pennsylvania Philadelphia, PA 19104 USA
3Department of Microbiology Monash University Clayton, Victoria Australia

Database Description

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species, and provides tools for cross-species comparisons. Sequence information is also integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE, and microarray projects. The relational schemas used to build PlasmoDB (GUS = Genomics Unified Schema and RAD = RNA Abundance Database) employ 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 version of the database is also available via CD-ROM (Plasmodium 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 data emerging from genome-scale projects by the global malaria research community.

Recent Developments

Over the past year PlasmoDB has expanded to include new data and new data types as well as changes to the site. The highlights of recent developments are: Automated gene predictions for all genomic P. falciparum sequence. Gene expression data consisting of oligo- and cDNA-based microArray and SAGE experiments. Draft genomic, GSS, and/or EST sequence for four additional Plasmodium species: P. berghei, P. chabaudi, P. vivax, and P. yoelii. Cross-species comparison between P. falciparum and P. yoelii. Optical and microsatellite mapping data. Updated interface, news, and tutorial sections of web site.

Acknowledgements

Financial support for PlasmoDB was provided by the Burroughs Wellcome Fund. Additional computational support was provided by Rahul Dave, Haralabos Tikos and the Eniac2000 project (supported in part through equipment donations from Intel). We thank the numerous researchers that have collaborated with and contributed to PlasmoDB by depositing data (both published and unpublished) in the database, by making software available, and by making useful suggestions on how to better improve this community resource. We wish to thank the scientists and funding agencies comprising the international Malaria Genome Project for making sequence data from the genome of P. falciparum (3D7) public prior to publication of the completed sequence. The Sanger Centre (UK) provided sequence for chromosomes 1, 3-9, & 13, with financial support from the Wellcome Trust. A consortium composed of The Institute for Genome Research, along with the Naval Medical Research Center (USA), sequenced chromosomes 2, 10, 11 & 14, with support from NIAID/NIH, the Burroughs Wellcome Fund, and the Department of Defense. The Stanford Genome Technology Center (USA) sequenced chromosome 12, with support from the Burroughs Wellcome Fund.

References

1. Fletcher,C. (1998) The Plasmodium falciparum Genome Project. Parasitology Today, 14, 342-344.
2. The Plasmodium Genome Database Collaborative (2001) PlasmoDB: an integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. Nucleic Acids Res., 29, 66-69.
3. Davidson, S., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G. C. and Stoeckert, C. J. Jr. (2001) K2/Klesli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal 40, 512-531.
4. Stoeckert, C., Pizarro, A., Manduchi, E., Gibson, M., Brunk, B., Crabtree, J., Schug, J., Shen-Orr, S. and Overton, C. G. (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17, 300-308.


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