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Nucleic Acids Research Advance Access originally published online on November 2, 2007
Nucleic Acids Research 2008 36(Database issue):D547-D552; doi:10.1093/nar/gkm820
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Nucleic Acids Research, 2008, Vol. 36, Database issue D547-D552
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

ProtozoaDB: dynamic visualization and exploration of protozoan genomes

Alberto M. R. Dávila1,*, Pablo N. Mendes9, Glauber Wagner1,2,3, Diogo A. Tschoeke1, Rafael R. C. Cuadrat1, Felipe Liberman1, Luciana Matos4, Thiago Satake11, Kary A. C. S. Ocaña1, Omar Triana1,10, Sérgio M. S. Cruz4,5, Henrique C. L. Jucá1, Juliano C. Cury1, Fabricio N. Silva4, Guilherme A. Geronimo2, Margarita Ruiz1, Eduardo Ruback1, Floriano P. Silva, Jr1, Christian M. Probst6, Edmundo C. Grisard2, Marco A. Krieger6, Samuel Goldenberg6, Maria C. R. Cavalcanti7, Milton O. Moraes1, Maria L. M. Campos8 and Marta Mattoso4

1Oswaldo Cruz Institute, FIOCRUZ, 2CCB, Federal University of Santa Catarina (UFSC), 3ACBS/UNOESC/SC, 4COPPE, Federal University of Rio de Janeiro, 5NCE, Federal University of Rio de Janeiro, 6Instituto de Biologia Molecular do Paraná, FIOCRUZ, 7Engineering Military Institute (IME), 8DCC, Federal University of Rio de Janeiro, Brazil, 9Knoesis Center, Wright State University, USA, 10Antioquia University, Colombia and 11Federal University of Paraná (UFPR), Brazil

*To whom correspondence should be addressed. Tel: +55 21 3865 8229; Fax: +55 21 3865 8229; Email: davila{at}fiocruz.br

Received August 15, 2007. Revised September 17, 2007. Accepted September 18, 2007.

ProtozoaDB (http://www.biowebdb.org/protozoadb) is being developed to initially host both genomics and post-genomics data from Plasmodium falciparum, Entamoeba histolytica, Trypanosoma brucei, T. cruzi and Leishmania major, but will hopefully host other protozoan species as more genomes are sequenced. It is based on the Genomics Unified Schema and offers a modern Web-based interface for user-friendly data visualization and exploration. This database is not intended to duplicate other similar efforts such as GeneDB, PlasmoDB, TcruziDB or even TDRtargets, but to be complementary by providing further analyses with emphasis on distant similarities (HMM-based) and phylogeny-based annotations including orthology analysis. ProtozoaDB will be progressively linked to the above-mentioned databases, focusing in performing a multi-source dynamic combination of information through advanced interoperable Web tools such as Web services. Also, to provide Web services will allow third-party software to retrieve and use data from ProtozoaDB in automated pipelines (workflows) or other interoperable Web technologies, promoting better information reuse and integration. We also expect ProtozoaDB to catalyze the development of local and regional bioinformatics capabilities (research and training), and therefore promote/enhance scientific advancement in developing countries.


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