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The rice genome is more than a tool for understanding the biology of a single species. It is a window into the structure and function of genes in the other crop grasses as well. Extensive work over the past two decades has shown a remarkably consistent conservation of large segments of linkage groups within rice, maize, sorghum, barley, wheat, rye, sugarcane and other agriculturally important grasses. A substantial body of data supports the notion that the rice genome is substantially colinear at both large and short scales with other crop grasses, opening the possibility of using rice synteny relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.
In other words, if the grasses are treated as a single family, one can expect to reap the benefits of a genome sequencing project for all of them based on actual sequencing of only one. By carefully identifying cross-species homology relationships, a ``benevolent cycle'' can be established. For example, information about the structure and function of a maize gene derived from classical genetic studies could be applied to a sequenced region of the rice genome in order to discover the function of a predicted rice gene. This information can in turn be used to pull out homologues in wheat and sorghum, which then can be fed back into the synteny map. As an information resource, Gramene will greatly facilitate researchers' ability to leverage the rice genomic sequence to identify and understand corresponding genes, pathways and phenotypes in the crop grasses.
The technological core of Gramene will be the Oracle database management system, a commercial relational database system that is stable and well-supported. We will develop a rational schema to represent the various biological entities of Gramene, and a middleware layer to dynamically translate this information into Web pages. Over the course of this project, we will migrate from the existing AceDB database (RiceGenes) to the Oracle database, doing so in such a way as to provide minimal disturbance to the data curators on the one hand, and the user community on the other. To facilitate the design and maintainence of the complex schema that will be required in this project, we will develop an object-oriented layer between the application layer and the database based on the Ensembl object model. The Ensembl object model is modular and has low-level hooks for accessing different types of databases, including relational databases as well as ACEDB.
Developers of the applications and the user interface will interact with the database via an object-oriented API similar to AcePerl, and behind the scenes, the object-oriented layer will silently translate queries into SQL statements and retrieve the requested data from Oracle.
Contact Information
Publications:
The following employment opportunities are available at Gramene:
Lincoln Stein lstein@cshl.org
Susan McCouch srm4@cornell.edu
Sam Cartinhour sc167@cornell.edu
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