Rice TE Database

The Rice TE Database has been developed at Arizona Genomics Institute. It collects repeated sequences and transposable elements (TEs) of several species of the Oryza (rice) genus, and the closely-related Leersia perrieri. Its goal is to assist and ease the repeat annotation - and consequent genomic analyses - of a multi-genome dataset developed for the Oryza Genome Evolution project, part of the International Oryza Map Alignment Project.

The database consists of annotated sequences organized in three sections:

the Plant Repeat Database (PReDA): a in house-developed set of (mostly plant) repeat and TE sequences;
de novo repeated sequences obtained with RepeatExplorer⁽¹⁾ using WGS Illumina data from 13 species;
a collection of complete TEs of most superfamilies isolated from sequence assemblies.

All sequences have been characterized adopting Wicker's classification code⁽²⁾ and extending it by encoding new TE superfamilies and non-TE repeats. Particular emphasis was given to the proper classification of sequences and to the removal of nested insertions.

The database is available for browsing and downloading sequences, as well as for aligning user-provided sequences against it.

August 31 2015: Version 1.1 has been released. After manual inspection, some sequences classified as LTR-RTs were removed since they were false positives.
July 1 2015: The RiTE-db manuscript has been accepted on BMC Genomics! The whole db content in its initial version (1.0) is publicly available.

^{⁽¹⁾ Novák P, Neumann P, Pech J, Steinhaisl J, Macas J: RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 2013, 29:792-793.}
^{⁽²⁾ Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH: A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8:973-982.}

This research was funded by National Science Foundation Plant Genome Award #1026200

Citation: Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing Y-I, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA: RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015, 16:538. doi:10.1186/s12864-015-1762-3

	Rice TE Database
Home Search BLAST Contact The Rice TE Database has been developed at Arizona Genomics Institute. It collects repeated sequences and transposable elements (TEs) of several species of the Oryza (rice) genus, and the closely-related Leersia perrieri. Its goal is to assist and ease the repeat annotation - and consequent genomic analyses - of a multi-genome dataset developed for the Oryza Genome Evolution project, part of the International Oryza Map Alignment Project. The database consists of annotated sequences organized in three sections: the Plant Repeat Database (PReDA): a in house-developed set of (mostly plant) repeat and TE sequences; de novo repeated sequences obtained with RepeatExplorer⁽¹⁾ using WGS Illumina data from 13 species; a collection of complete TEs of most superfamilies isolated from sequence assemblies. All sequences have been characterized adopting Wicker's classification code⁽²⁾ and extending it by encoding new TE superfamilies and non-TE repeats. Particular emphasis was given to the proper classification of sequences and to the removal of nested insertions. The database is available for browsing and downloading sequences, as well as for aligning user-provided sequences against it. August 31 2015: Version 1.1 has been released. After manual inspection, some sequences classified as LTR-RTs were removed since they were false positives. July 1 2015: The RiTE-db manuscript has been accepted on BMC Genomics! The whole db content in its initial version (1.0) is publicly available. ^{⁽¹⁾ Novák P, Neumann P, Pech J, Steinhaisl J, Macas J: RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 2013, 29:792-793.} ^{⁽²⁾ Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH: A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8:973-982.} This research was funded by National Science Foundation Plant Genome Award #1026200 Citation: Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing Y-I, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA: RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015, 16:538. doi:10.1186/s12864-015-1762-3
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