PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a compre- hensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16000 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 develop- ment 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 struc- ture also permits easy integration with other data types and opens up prospects for future implementations.
PRGdb: a bioinformatics platform for plant resistance gene analysis / Sanseverino, W.; Roma, G.; De Simone, M.; Faino, L.; Melito, S.; Stupka, E.; Frusciante, Luigi; Ercolano, MARIA RAFFAELLA. - In: NUCLEIC ACIDS RESEARCH. - ISSN 0305-1048. - STAMPA. - (2010), pp. 1-8. [10.1093/nar/gkp978]
PRGdb: a bioinformatics platform for plant resistance gene analysis
FRUSCIANTE, LUIGI;ERCOLANO, MARIA RAFFAELLA
2010
Abstract
PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a compre- hensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16000 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 develop- ment 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 struc- ture also permits easy integration with other data types and opens up prospects for future implementations.File | Dimensione | Formato | |
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