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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS Title: CottonDB enhancement

Authors
item Yu, Jing - TAMU
item Kohel, Russell - ARS COLLABORATOR
item Hinze, Lori
item Frelichowski, James
item Xu, Zhanyou - TAMU
item Yu, John
item Percy, Richard

Submitted to: International Cotton Genome Initiative Workshop
Publication Type: Abstract Only
Publication Acceptance Date: June 15, 2008
Publication Date: July 8, 2008
Citation: Yu, J., Kohel, R.J., Hinze, L.L., Frelichowski, J.E., Xu, Z., Yu, J., Percy, R.G. 2008. CottonDB enhancement [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, July 8-11, 2008, Anyang, China. p. 120.

Technical Abstract: CottonDB (www.cottondb.org) was initiated in 1995. It is a database that contains genomic, genetic, and taxonomic information for cotton (Gossypium spp.). It serves both as an archival database and as a dynamic database, which incorporates new data and user resources. CottonDB is maintained at the Southern Plains Agricultural Research Center in College Station, TX. The project includes a website and database creating a repository of information for over 450,000 gene, EST, and contig sequences; genetic and physical map data; nearly 10,000 DNA primers; and 9,000 germplasm accessions. Tens of genetic maps and data of trait studies have been updated. The 13-year-old database is now being migrated to a new database architecture, and the new user interface provides a more intuitive approach to searching. Several graphical interfaces have been or will be implemented. CMap viewer, developed by Gramene, has been used to facilitate comparative genomics in CottonDB by allowing users to align and compare all maps in CottonDB; web BLAST server, developed by NCBI, complemented by 18 cotton and Arabidopsis nucleotide and protein sequence databases, is used for comparing gene and protein sequences against others in public databases; web FPC Viewer, developed by Arizona Genomics Institute, has been used for displaying cotton BAC clone contigs and cotton physical maps and for the assembly of sequence ready clones for large scale sequencing projects; and GBrowse, developed by GMOD, will provide a user-friendly interface for physical maps and allow users to annotate map data. An overview of current accessions, new features, and planned additions will be presented. An open invitation is extended to the research community to make suggestions, contribute data, and develop tools to improve the performance and utility of this public database.

Last Modified: 10/24/2014
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