STINGRAY: system for integrated genomic resources and analysis

BMC Research Notes

Alberto MR Dávila⁵  Marta Mattoso⁴  Maria LM Campos¹  Maria C Cavalcanti²  Edmundo C Grisard⁹  André N Pitaluga³  Christian M Probst⁶  Vanessa E Emmel⁸  Antonio CB Ribeiro³  Kary ACS Ocaña⁵  Daniel R Loureiro⁵  Diogo A Tschoeke⁵  Rodrigo Jardim⁵  Glauber Wagner⁷ 

[1] Instituto de Matemática, Departamento de Ciência da Computação, Universidade Federal do Rio de Janeiro, Bloco C, CCMN, Sala E-2206, Ilha do Fundão, 21945-970 Rio de Janeiro, Rio de Janeiro, Brazil;Instituto Militar de Engenharia (IME), Seção de Engenharia de Computação (SE-8), Praça General Tibúrcio 80, Praia Vermelha, Urca, 22290-270 Rio de Janeiro, Rio de Janeiro, Brazil;Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, 21040-360 Rio de Janeiro, Rio de Janeiro, Brazil;Instituto Alberto Luiz Coimbra de Pós-graduação e Pesquisa de Engenharia (COPPE), Universidade Federal do Rio de Janeiro, P.O. Box 68511, Ilha do Fundão, 21941-972 Rio de Janeiro, Rio de Janeiro, Brazil;Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, 21040-360 Rio de Janeiro, Rio de Janeiro, Brazil;Laboratório de Bioinformática, Instituto Carlos Chagas (ICC), Fundação Oswaldo Cruz (FIOCRUZ), Avenida Algacyr Munhoz Mader, 3775, Cidade Industrial, 81350-010 Curitiba, Paraná, Brazil;Laboratório de Doenças Infecciosas e Parasitárias (LDIP), Área de Ciências Biológicas e da Saúde (ACBS), Universidade do Oeste de Santa Catarina (Unoesc), Rua Getúlio Vargas 2125, Flor da Serra, 89600-000 Joaçaba, Santa Catarina, Brazil;Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, 21040-360 Rio de Janeiro, Rio de Janeiro, Brazil;Laboratório de Protozoologia, Departamento de Microbiologia, Imunologia e Parasitologia (MIP), Centro de Ciências Biológicas (CCB), Universidade Federal de Santa Catarina (UFSC), Campus Universitário, Setor F, Bloco A, Trindade, 88040-970, Caixa Postal 476, Florianópolis, Santa Catarina, Brazil

关键词: Data integration;    Sanger;    Next generation sequencing;    Workflow;    Annotation;    Genome;   

Others  :  1134354
DOI  :  10.1186/1756-0500-7-132

 received in 2013-10-16, accepted in 2014-02-28,  发布年份 2014

【 摘 要 】

Background

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms.

Findings

STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation.

Conclusion

STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available athttp://stingray.biowebdb.org webcite and the open source code athttp://sourceforge.net/projects/stingray-biowebdb/ webcite.

【 授权许可】

   
2014 Wagner et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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