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CastorDB: A comprehensive knowledge base for Ricinus communis

BMC Research Notes 2011年第1期4卷 1-9页

作者： Thakur, Shalabh Jha, Sanjay Chattoo, Bharat B. Centre for Genome Research Department of Microbiology and Biotechnology Centre M. S. University of Baroda Vadodara-390002 India Department of Biotechnology ASPEE College of Horticulture and Forestry Navsari Agricultural University Navsari Gujarat-396450 India

Background: Ricinus communis is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, R. communis genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of R. communis is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant. Findings. CastorDB is a specialized and comprehensive database for the oil seed plant R. communis, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein. Conclusion: CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners. © 2011 Chattoo et al;licensee BioMed Central Ltd.

关键词： Application Program Interface Ricinus Communis interact protein Pair Sumoylation Site protein interact partner

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