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EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

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Autor(es):
Nascimento, Leandro Costa [1, 2] ; Salazar, Marcela Mendes [1] ; Lepikson-Neto, Jorge [1] ; Oliveira Camargo, Eduardo Leal [1] ; Parreiras, Lucas Salera [1] ; Guimaraes Pereira, Goncalo Amarante [1] ; Carazzolle, Marcelo Falsarella [1, 3]
Número total de Autores: 7
Afiliação do(s) autor(es):
[1] Univ Estadual Campinas, Inst Biol, Dept Genet Evolucao & Bioagentes, LGE, Campinas, SP - Brazil
[2] Univ Estadual Campinas, LaCTAD, Campinas, SP - Brazil
[3] Univ Estadual Campinas, Ctr Nacl Processamento Alto Desempenho Sao Paulo, Campinas, SP - Brazil
Número total de Afiliações: 3
Tipo de documento: Artigo Científico
Fonte: DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION; OCT 24 2017.
Citações Web of Science: 0
Resumo

Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrys needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. (AU)

Processo FAPESP: 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais
Beneficiário:Munir Salomao Skaf
Linha de fomento: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs