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SchistoDB


NAR Molecular Biology Database Collection entry number 1219
Zerlotini, A.1,2, Heiges, M.2, Wang, H.2, Moraes, R.L.V.1, Dominitini, A.J.1, Ruiz, J.C.1, Kissinger, J.C.2,3 Oliveira, G.1
1Laboratorio de Parasitologia Celular e Molecular, Instituto Rene Rachou, FIOCRUZ, Brasil.2Center for Tropical and Emerging Global Diseases, University of Georgia, U.S.3Department of Genetics, University of Georgia, U.S.

Database Description

SchistoDB (http://SchistoDB.net) is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide (1,2). It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, ORFs, metabolic pathways and drugs. The computational analysis we provide has helped genome annotation. The construction of a relational database containing the parasite genomic data enables us to perform and combine approximately 30 different queries and also provided access to several tools for analyzing, retrieving or viewing the data such as BLAST, PathwayTools (3) and GMOD Genome Browser (4).
One highlight of the database is its integration to the metabolic pathway prediction generated using the SRI PathwayTools software (3). Pathway analysis allowed us to select putative drug target candidates. The database also contains all drugs available on the Kegg drug database (5), thus enabling us to indicate enzymes known to be targeted in other organisms.

Acknowledgements

The authors would like to acknowledge the genome sequencing consortium, TIGR, and WTSI for the availability of the genome assembly and annotation of S. mansoni. Without their generous pre-publication contribution, this integrated database resource would not be possible. Special thanks to the GUS developers and to the EupathDB group, that provided essential support to accomplish this work. This work was supported by the National Institutes of Health - Fogarty International Center [5D43TW007012-03].

References

1. WHO (accessed July 15, 2008) Schistosomiasis. http://www.who.int/mediacentre/factsheets/fs115/en/index.html.
2. Chitsulo, L., Engels, D., Montresor, A. and Savioli, L. (2000) The global status of schistosomiasis and its control. Acta Trop., 77, 41-51.
3. Karp, P.D., Paley, S. and Romero, P. (2002) The Pathway Tools software. Bioinformatics, 18 Suppl 1, S225-32.
4. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res, 12, 1599-1610.
5. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res, 36, D480-4.


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