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Bioinformatics Advance Access originally published online on October 6, 2005
Bioinformatics 2005 21(23):4302-4303; doi:10.1093/bioinformatics/bti705
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

GARSA: genomic analysis resources for sequence annotation

Alberto M. R. Dávila 1,6,*, Daniel M. Lorenzini 2, Pablo N. Mendes 3, Thiago S. Satake 4, Gabriel R. Sousa 1,6, Linair M. Campos 3, Camila J. Mazzoni 1, Glauber Wagner 1,6, Paulo F. Pires 3, Edmundo C. Grisard 2, Maria C. R. Cavalcanti 5 and Maria Luiza M. Campos 3

1DBBM, Instituto Oswaldo Cruz Fiocruz, Brazil
2Laboratório de Bioinformática and Laboratório de Protozoologia—MIP/CCB, Universidade Federal de Santa Catarina Brazil
3Departamento de Ciência da Computação/Núcleo de Computação Eletrônica—UFRJ Brazil
4Engenharia de Bioprocessos e Biotecnologia, Universidade Federal do Paraná Brazil
5Instituto Militar de Engenharia Brazil
6Bioinformatics and Molecular Evolutionary Genetics Group Brazil

*To whom correspondence should be addressed.

Summary: Growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools and genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analyzed using the system since it accepts (1) chromatograms, (2) download of sequences from GenBank, (3) Fasta files stored locally or (4) a combination of all three. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), Trypanosoma rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST).

Availability: The GARSA system is freely available under GPL license (http://www.biowebdb.org/garsa/). For download requests visit http://www.biowebdb.org/garsa/ or contact Dr Alberto Dávila.

Contact: davila{at}fiocruz.br

Received on July 10, 2005; revised on September 7, 2005; accepted on October 5, 2005

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