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Open Access Highly Accessed Database

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research

Sook Jung12, Christopher Jesudurai12, Margaret Staton12, Zhidian Du2, Stephen Ficklin12, Ilhyung Cho3, Albert Abbott1, Jeffrey Tomkins12 and Dorrie Main12*

Author Affiliations

1 Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

2 Clemson University Genomics Institute, Clemson University, Clemson, SC, 29634, USA

3 Department of Computer Sciences, Saginaw Valley State University, University Center, MI, 48710, USA

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BMC Bioinformatics 2004, 5:130  doi:10.1186/1471-2105-5-130

Published: 9 September 2004

Abstract

Background

Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools.

Description

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity.

Conclusions

The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/ webcite.