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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #219937

Title: CottonDB: Cotton Genome Database

item Hinze, Lori
item Frelichowski, James - Jim
item Yu, John
item Kohel, Russell

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/5/2007
Publication Date: 1/13/2008
Citation: Yu, J., Hinze, L.L., Frelichowski, J.E., Xu, Z., Yu, J., Kohel, R.J. 2008. CottonDB: Cotton Genome Database [abstract]. In: Proceedings of Plant and Animal Genome Conference XVI, January 12-16, 2007, San Diego, California. Paper No. W253.

Interpretive Summary:

Technical Abstract: CottonDB ( is the first and most comprehensive source of cotton genome information. 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 355,000 gene, EST, and contig sequences; genetic and physical map data; 8,000 DNA primers; and 9,000 germplasm accessions. The 12-year-old database is now migrating to a relational database architecture, and the new user interface provides a more intuitive approach to searching. Several graphic 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 the CottonDB and curators to include more features than currently available with the ACEDB map viewer; web BLAST server, developed by NCBI, complemented by 15 cotton and Arabidopsis nucleotide and protein sequence databases, is used for comparing gene and protein sequences against other public databases; web PFC 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 GBrowser, 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 suggest improvements, contribute data, and develop tools to better serve this public database.