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Nucleic Acids Research, 2004, Vol. 32, Database issue D360-D363
© 2004 Oxford University Press

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants

Shu Ouyang and C. Robin Buell*

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +1 301 838 3558; Fax: +1 301 838 0208; Email: rbuell{at}tigr.org

In a number of higher plants, a substantial portion of the genome is composed of repetitive sequences that can hinder genome annotation and sequencing efforts. To better understand the nature of repetitive sequences in plants and provide a resource for identifying such sequences, we constructed databases of repetitive sequences for 12 plant genera: Arabidopsis, Brassica, Glycine, Hordeum, Lotus, Lycopersicon, Medicago, Oryza, Solanum, Sorghum, Triticum and Zea (www.tigr.org/tdb/e2k1/plant. repeats/index.shtml). The repetitive sequences within each database have been coded into super-classes, classes and sub-classes based on sequence and structure similarity. These databases are available for sequence similarity searches as well as downloadable files either as entire databases or subsets of each database. To further the utility for comparative studies and to provide a resource for searching for repetitive sequences in other genera within these families, repetitive sequences have been combined into four databases to represent the Brassicaceae, Fabaceae, Gramineae and Solanaceae families. Collectively, these databases provide a resource for the identification, classification and analysis of repetitive sequences in plants.


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