title: DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.
abstract: 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.
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Brazil. wcsmagalhaes@gmail.com
authors.forename: Wagner C S
authors.initials: WC
authors.lastname: Magalhães
authors.forename: Maíra R
authors.initials: MR
authors.lastname: Rodrigues
authors.forename: Donnys
authors.initials: D
authors.lastname: Silva
authors.forename: Giordano
authors.initials: G
authors.lastname: Soares-Souza
authors.forename: Márcia L
authors.initials: ML
authors.lastname: Iannini
authors.forename: Gustavo C
authors.initials: GC
authors.lastname: Cerqueira
authors.forename: Alessandra C
authors.initials: AC
authors.lastname: Faria-Campos
authors.forename: Eduardo
authors.initials: E
authors.lastname: Tarazona-Santos
mesh_terms: D000465:Algorithms; D001331:Automation; D001938:Brazil; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D055106:Genome-Wide Association Study; D051275:Glucose Transporter Type 4 / Q000235:genetics; D006801:Humans; D020407:Internet; D017720:Molecular Epidemiology; D010641:Phenotype; D012984:Software
chemical_list: D051275:Glucose Transporter Type 4; C495692:SLC2A4 protein, human