DIVERGENOME: A Bioinformatics Platform to Assist Population Genetics and Genetic Epidemiology Studies

Large‐scale genomics initiatives such as the HapMap project and the 1000‐genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from diff...

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Published in:Genetic epidemiology 2012-05, Vol.36 (4), p.360-367
Main Authors: Magalhães, Wagner C. S., Rodrigues, Maíra R., Silva, Donnys, Soares-Souza, Giordano, Iannini, Márcia L., Cerqueira, Gustavo C., Faria-Campos, Alessandra C., Tarazona-Santos, Eduardo
Format: Article
Language:English
Subjects:
Algorithms
Automation
Brazil
Computational Biology - methods
Databases, Genetic
format conversion
genetic epidemiology
Genetic Variation
Genetics, Population
Genome, Human
Genome-Wide Association Study
Glucose Transporter Type 4 - genetics
Humans
Internet
Molecular Epidemiology
Phenotype
population genetics
Software
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Summary:Large‐scale genomics initiatives such as the HapMap project and the 1000‐genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from different sources, as well as to assist these scientists to perform their analyses efficiently. We developed such a bioinformatics platform, DIVERGENOME, to assist population genetics and genetic epidemiology studies performed by small‐ to medium‐sized research groups. The platform is composed of two integrated components, a relational database (DIVERGENOMEdb), and a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology (DIVERGENOMEtools). In DIVERGENOMEdb, information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in projects. These can be queried according to permissions. Here, we validated DIVERGENOME through a use case regarding the analysis of SLC2A4 genetic diversity in human populations. DIVERGENOME, with its intuitive Web interface and automatic data loading capability, facilitates its use by individuals without bioinformatics background, allowing complex queries to be easily interrogated and straightforward data format conversions (not available in similar platforms). DIVERGENOME is open source, freely available, and can be accessed online (pggenetica.icb.ufmg.br/divergenome) or hosted locally. Genet. Epidemiol. 36:360–367, 2012. © 2012 Wiley Periodicals, Inc.
ISSN:0741-0395
1098-2272
DOI:10.1002/gepi.21629