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Nucleic Acids Research 2006 34(Database Issue):D741-D744; doi:10.1093/nar/gkj094
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Nucleic Acids Research, 2006, Vol. 34, Database issue D741-D744
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

Hajime Ohyanagi1,2, Tsuyoshi Tanaka3, Hiroaki Sakai3, Yasumasa Shigemoto1,4, Kaori Yamaguchi5, Takuya Habara5,6, Yasuyuki Fujii5,6, Baltazar A. Antonio3, Yoshiaki Nagamura3, Tadashi Imanishi6, Kazuho Ikeo1, Takeshi Itoh3,6,*, Takashi Gojobori1,6 and Takuji Sasaki3

1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems 1111 Yata, Mishima, Shizuoka 411-8540, Japan 2Tsukuba Division, Mitsubishi Space Software Co., Ltd 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan 3Genome Research Department, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan 4Life Science Systems Division, Fujitsu Limited 1-17-25 Shinkamata, Ota-ku, Tokyo 144-8588, Japan 5Japan Biological Information Research Center, Japan Biological Informatics Consortium 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 6Biological Information Research Center, National Institute of Advanced Industrial Science and Technology 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan

*To whom correspondence should be addressed. Tel: +81 29 838 7065; Fax: +81 29 838 7065; Email: taitoh{at}affrc.go.jp

Received August 15, 2005. Revised October 16, 2005. Accepted October 16, 2005.

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.


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