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BMC Genomics. 2009; 10: 14.
Published online 2009 January 9. doi:  10.1186/1471-2164-10-14
PMCID: PMC2645430

RepPop: a database for repetitive elements in Populus trichocarpa

Abstract

Background

Populus trichocarpa is the first tree genome to be completed, and its whole genome is currently being assembled. No functional annotation about the repetitive elements in the Populus trichocarpa genome is currently available.

Results

We predicted 9,623 repetitive elements in the Populus trichocarpa genome, and assigned functions to 3,075 of them (31.95%). The 9,623 repetitive elements cover ~40% of the current (partially) assembled genome. Among the 9,623 repetitive elements, 668 have copies only in the contigs that have not been assigned to one of the 19 chromosome while the rest all have copies in the partially assembled chromosomes.

Conclusion

All the predicted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.


Articles from BMC Genomics are provided here courtesy of BioMed Central
 
{"cc_re__cc_re__cc_by_2_0": ["e\"><div class=\"fm-pubdate half_rhythm\">Received 2008 June 4; Accepted 2009 January 9.</div></div><div class=\"fm-cpl-info fm-panel hide half_rhythm\" id=\"id1605093_cpl\" style=\"display:none\"><div class=\"fm-copyright half_rhythm\"><a href=\"/pmcc/static/copyright/\">Copyright</a>  &#x000a9; 2009 Zhou and Xu; licensee BioMed Central Ltd.</div><div class=\"fm-copyright half_rhythm\"><p id=\"__pid1245810\">This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<a href=\"http://creativecommons.org/licenses/by/2.0\" ref=\"reftype=extlink&amp;article-id=126410&amp;issue-id=4717&amp;journal-id=49&amp;FROM=Article%7CFront%20Matter&amp;TO=External%7CLink%7CURI&amp;rendering-type=normal\" target=\"pmc_ext\">http://creativecommons.org/licenses/by/2.0</a>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p></div></div></div><div class=\"links-box fm-panel whole_rhythm\"><div class=\"small\"><div>This article has been <a href=\"/pmcc/articles/PMC2645430/citedby/\">cited by</a> other articles in PMC.</div></div></div></div><div class=\"sec\"></div><div id=\"__abstractid1245822\" class=\"sec\"><h2 class=\"head no_bottom_margin\" id=\"__abstra"], "copyright__copyright__copyright": ["ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0", "ted data are organized into an easy-to-use web-browsable database, RepPop. Various search capabilities are provided against the RepPop database. A Wiki system has been set up to facilitate functional annotation and curation of the repetitive elements by a community rather than just the database developer. The database RepPop will facilitate the assembling and functional characterization of the Populus trichocarpa genome.\n\n\nArticles from BMC Genomics are provided here courtesy of BioMed Central\n\u00a0"]}