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The Rice Annotation Project Database (RAP-DB): 2008 update.


ABSTRACT: The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

SUBMITTER: Rice Annotation Project 

PROVIDER: S-EPMC2238920 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

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The Rice Annotation Project Database (RAP-DB): 2008 update.

Tanaka Tsuyoshi T   Antonio Baltazar A BA   Kikuchi Shoshi S   Matsumoto Takashi T   Nagamura Yoshiaki Y   Numa Hisataka H   Sakai Hiroaki H   Wu Jianzhong J   Itoh Takeshi T   Sasaki Takuji T   Aono Ryo R   Fujii Yasuyuki Y   Habara Takuya T   Harada Erimi E   Kanno Masako M   Kawahara Yoshihiro Y   Kawashima Hiroaki H   Kubooka Hiromi H   Matsuya Akihiro A   Nakaoka Hajime H   Saichi Naomi N   Sanbonmatsu Ryoko R   Sato Yoshiharu Y   Shinso Yuji Y   Suzuki Mami M   Takeda Jun-ichi J   Tanino Motohiko M   Todokoro Fusano F   Yamaguchi Kaori K   Yamamoto Naoyuki N   Yamasaki Chisato C   Imanishi Tadashi T   Okido Toshihisa T   Tada Masahito M   Ikeo Kazuho K   Tateno Yoshio Y   Gojobori Takashi T   Lin Yao-Cheng YC   Wei Fu-Jin FJ   Hsing Yue-ie YI   Zhao Qiang Q   Han Bin B   Kramer Melissa R MR   McCombie Richard W RW   Lonsdale David D   O'Donovan Claire C CC   Whitfield Eleanor J EJ   Apweiler Rolf R   Koyanagi Kanako O KO   Khurana Jitendra P JP   Raghuvanshi Saurabh S   Singh Nagendra K NK   Tyagi Akhilesh K AK   Haberer Georg G   Fujisawa Masaki M   Hosokawa Satomi S   Ito Yukiyo Y   Ikawa Hiroshi H   Shibata Michie M   Yamamoto Mayu M   Bruskiewich Richard M RM   Hoen Douglas R DR   Bureau Thomas E TE   Namiki Nobukazu N   Ohyanagi Hajime H   Sakai Yasumichi Y   Nobushima Satoshi S   Sakata Katsumi K   Barrero Roberto A RA   Sato Yutaka Y   Souvorov Alexandre A   Smith-White Brian B   Tatusova Tatiana T   An Suyoung S   An Gynheung G   OOta Satoshi S   Fuks Galina G   Fuks Galina G   Messing Joachim J   Christie Karen R KR   Lieberherr Damien D   Kim HyeRan H   Zuccolo Andrea A   Wing Rod A RA   Nobuta Kan K   Green Pamela J PJ   Lu Cheng C   Meyers Blake C BC   Chaparro Cristian C   Piegu Benoit B   Panaud Olivier O   Echeverria Manuel M  

Nucleic acids research 20071217 Database issue


The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional gen  ...[more]

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