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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps

Authors
item Andorf, Carson
item Lawrence, Carolyn
item Harper, Elisabeth
item Schaeffer, Mary
item Campbell, Darwin
item Sen, Taner

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 11, 2009
Publication Date: February 1, 2010
Citation: Andorf, C.M., Lawrence, C.J., Harper, E.C., Schaeffer, M.L., Campbell, D.A., Sen, T.Z. 2010. The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps. Bioinformatics. 26(3):434-436.

Interpretive Summary: The Maize Genetics and Genomics Database (MaizeGDB) is the community resource for maize data and can be accessed online at http://www.maizegdb.org. The maize genome is being sequenced, and the outcomes of the sequencing project are being made available on a continuous basis. However, the bioinformatic tools needed to integrate sequence with existing map information are insufficient. To address this need, we developed the Locus Lookup Tool that enables researchers to identify genomic regions. Using this tool, researchers are able to locate specific genes that ultimately will help them to develop a better corn plant. Ultimately, growers will benefit from this technology as healthier and higher-yielding corn plants are developed.

Technical Abstract: Methods to automatically integrate sequence information with physical and genetic maps are scarce. The Locus Lookup Tool enables researchers to define windows of genomic sequence likely to contain loci of interest where only genetic or physical mapping associations are reported. Using the Locus Lookup tool, researchers will be able to locate specific genes more efficiently that will ultimately help them develop a better maize plant. With the availability of the well-documented source code, the tool can be easily adapted to other biological systems.

Last Modified: 12/18/2014