Bioinformatics Advance Access originally published online on October 4, 2005
Bioinformatics 2005 21(23):4307-4308; doi:10.1093/bioinformatics/bti698
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OxfordGrid: a web interface for pairwise comparative map views
Center for Applied Genetic Technologies, University of Georgia 111 Riverbend Road, Athens, GA 30602, USA
*To whom correspondence should be addressed.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONDESCRIPTIONREFERENCES |
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Summary: OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information.
Availability: OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/
Contact: agingle{at}uga.edu
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONDESCRIPTIONREFERENCES |
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OxfordGrid was initially developed to provide comparative views of orthologous loci for our cotton (http://cotton.agtec.uga.edu/OxfordGrid/index.aspx) and CGGC/sorghum (http://cggc.agtec.uga.edu/oxfordgrid/images.aspx) database resources. Its development, motivated by the need to provide real-time Oxford grid generation and relational database (RDBMS) compatibility, benefited from collaboration with practical genetic mappers developing high-density genetic maps for cotton (Rong et al., 2004) and sorghum (Bowers et al., 2003). The dynamic image map-based interface facilitates real-time interactive features like ‘linear selection mode’ that allows users to identify syntenic regions and list their associated probes. Other applications that generate Oxford grids for genetic map or similar dot-plots for genomic sequence data have been developed (e.g. Brodie et al., 2004; Edwards, 1991; Huang and Zhang, 2004); however, they are not compatible with our strategy of implementing real-time interactive features that are compatible with a broad range of web browsers and do not require client-side software additions. Our approach has led to the development of a MySQL compatible web application that provides a compact and interactive Oxford Grid interface and database. Like its CGGC counterpart, the application can also be configured to serve as a portal to other web resources with the configuration details described in the installation document (ftp://cggc.agtec.uga.edu/OxfordGrid/readme.pdf).
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DESCRIPTION |
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TOPABSTRACTINTRODUCTIONDESCRIPTIONREFERENCES |
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OxfordGrid is a web application that generates an interactive Oxford grid (Edwards, 1991) display for the study of genome organization from comparative genetic map data. It is composed of a matrix of grid cells, each representing a pairwise comparison of map data for linkage group pairs. The linkage groups are arranged along the axes with one forming cell columns and the other cell rows. A dot inside a cell represents a molecular marker/probe that has been mapped to both linkage groups with its coordinates being the associated map locations. The degree and the pattern of synteny between the two linkage groups are manifested in the dot density and pattern within the cell. This is especially true for high-density maps where inserts can be detected and orientation established based on the presence and slope of linear segments in the dot pattern. Of course, chromosomal duplications are apparent as well.
Using OxfordGrid to compare two linkage groups is a multistep process. Combinations of maps/species are selected from a menu, which launches the multicell display (Fig. 1A), providing a comparative overview for all linkage group pairs. A detailed view of a particular linkage group pair (Fig. 1B) can be launched with a mouse click over its associated cell as indicated by the arrow. This view provides two types of queries. In the point mode, each dot is an interactive link that can be configured to navigate either directly to a detailed probe information page or via a list of probes when more than one are associated with a single dot's map coordinates. All navigation is automatic with the configuration details described in the installation package's readme file. In the linear mode, users can, with mouse clicks, select endpoints of an identified linear segment (Fig. 1B). The interface then superimposes a line segment between the endpoints, highlights the dots on or near the linear segment and displays a list of the associated probe hyperlinks, which are also configurable (Fig. 1C).
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OxfordGrid is an ASP.NET (Microsoft) web application and is compatible with the Windows Internet Information Server (IIS). The Oxford grid images are generated, on the fly, as bitmap objects using the .NET framework's drawing classes and the interactive features of the interface are implemented using classic HTML image maps. It is a data-driven application and the downloadable version is compatible with a MySQL RDBMS back-end. The associated schema contains tables to accommodate map, synteny and taxonomy-related data as well as configurable URL/navigation information. The table for synteny data can become quite large as the number of possible map pairs increases and, therefore, indexes are employed for species and linkage group. Detailed information on the schema is available in the installation package readme file. Also, to extend OxfordGrid's application range, we have developed scripts for importing relevant data from the GMOD/CMap (http://www.gmod.org/cmap/index.shtml) database schema and these are included in the installation package along with instructions on their use and integration into data processing pipelines. Information is also included on the data mappings between the two schemas.
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Acknowledgments |
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The authors wish to thank the collaborating laboratories for providing data and advice. We are grateful to the National Science Foundation, the United States Department of Agriculture, the Georgia Research Alliance, the National Grain Sorghum Producers and the University of Georgia Research Foundation for financial support.
Conflict of Interest: none declared.
Received on August 5, 2005; revised on September 27, 2005; accepted on September 27, 2005
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REFERENCES |
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TOPABSTRACTINTRODUCTIONDESCRIPTIONREFERENCES |
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Bowers, J.E., et al. (2003) A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics, 165, 367–386
Brodie, R., et al. (2004) Jdotter: a Java interface to multiple dotplots generated by dotter. Bioinformatics, 20, 279–281
Edwards, J.H. (1991) The Oxford grid. Ann. Hum. Genet, . 55, 17–31[Medline].
Huang, Y. and Zhang, L. (2004) Rapid and sensitive dot-matrix methods for genome analysis. Bioinformatics, 20, 460–466
Rong, J., et al. (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics, 166, 389–417
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