Tuesday, November 06, 2007

ProtozoaDB: dynamic visualization and exploration of protozoan genomes

Nucleic Acids Res. 2007 Nov 2; [Epub ahead of print]

ProtozoaDB: dynamic visualization and exploration of protozoan genomes

Dávila AM, Mendes PN, Wagner G, Tschoeke DA, Cuadrat RR, Liberman F, Matos L, Satake T, Ocaña KA, Triana O, Cruz SM, Jucá HC, Cury JC, Silva FN, Geronimo GA, Ruiz M, Ruback E, Silva FP Jr, Probst CM, Grisard EC, Krieger MA, Goldenberg S, Cavalcanti MC, Moraes MO, Campos ML, Mattoso M

Oswaldo Cruz Institute, FIOCRUZ, CCB, Federal University of Santa Catarina (UFSC), ACBS/UNOESC/SC, COPPE, Federal University of Rio de Janeiro, NCE, Federal University of Rio de Janeiro, Instituto de Biologia Molecular do Paraná, FIOCRUZ, Engineering Military Institute (IME), DCC, Federal University of Rio de Janeiro, Brazil, Knoesis Center, Wright State University, USA, Antioquia University, Colombia and Federal University of Paraná (UFPR), Brazil.

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.

PMID: 17981844 [PubMed - as supplied by publisher]

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