title: PRGdb: a bioinformatics platform for plant resistance gene analysis.
abstract: PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations.
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, Italy.
authors.forename: Walter
authors.initials: W
authors.lastname: Sanseverino
authors.forename: Guglielmo
authors.initials: G
authors.lastname: Roma
authors.forename: Marco
authors.initials: M
authors.lastname: De Simone
authors.forename: Luigi
authors.initials: L
authors.lastname: Faino
authors.forename: Sara
authors.initials: S
authors.lastname: Melito
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
authors.forename: Luigi
authors.initials: L
authors.lastname: Frusciante
authors.forename: Maria Raffaella
authors.initials: MR
authors.lastname: Ercolano
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D018384:Oxidative Stress; D010935:Plant Diseases / Q000235:genetics*; D010944:Plants / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012984:Software; D014584:User-Computer Interface