Abstract
BackgroundRicinus 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.FindingsCastorDB 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.ConclusionCastorDB 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.
Highlights
Ricinus communis (Euphorbiaceae family) is an industrially important non-edible oil seed crop with several well established applications in industry
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
The mapping of GO annotation to Pfam Domain was generated from data available from InterPro database for InterPro2GO mapping [9]. 11847 proteins were mapped with probable GO annotation in R. communis
Summary
Ricinus communis (Euphorbiaceae family) is an industrially important non-edible oil seed crop with several well established applications in industry. Sequence data of Castor bean plant was obtained from various resources like National Center for Biotechnology Information (NCBI) [2] and JCVI Castor Bean Genome Database [3]. Primary Data Sequence Data Sequence information on 31,221 proteins and genes of R. communis was downloaded from JCVI Castor Genome database [3] on January 12, 2009. Sequences from this database have unique locus identifiers, which were used during the analysis for distinguishing sequences from each other. 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 comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant
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