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Nucleic Acids Res. 2004 Jan 1;32(Database issue):D360-3.

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

Author information

1
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

Abstract

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.

PMID:
14681434
PMCID:
PMC308833
DOI:
10.1093/nar/gkh099
[Indexed for MEDLINE]
Free PMC Article

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