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

Tanaka, T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Souvorov A, Smith-White B, Tatusova T, An S, An G, S OO, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.  2008.  

Journal:

Nucleic Acids Res

Volume Number:

36

Pages:

D1028-33

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/.

Notes:

Rice Annotation ProjectTanaka, TsuyoshiAntonio, Baltazar AKikuchi, ShoshiMatsumoto, TakashiNagamura, YoshiakiNuma, HisatakaSakai, HiroakiWu, JianzhongItoh, TakeshiSasaki, TakujiAono, RyoFujii, YasuyukiHabara, TakuyaHarada, ErimiKanno, MasakoKawahara, YoshihiroKawashima, HiroakiKubooka, HiromiMatsuya, AkihiroNakaoka, HajimeSaichi, NaomiSanbonmatsu, RyokoSato, YoshiharuShinso, YujiSuzuki, MamiTakeda, Jun-ichiTanino, MotohikoTodokoro, FusanoYamaguchi, KaoriYamamoto, NaoyukiYamasaki, ChisatoImanishi, TadashiOkido, ToshihisaTada, MasahitoIkeo, KazuhoTateno, YoshioGojobori, TakashiLin, Yao-ChengWei, Fu-JinHsing, Yue-ieZhao, QiangHan, BinKramer, Melissa RMcCombie, Richard WLonsdale, DavidO'Donovan, Claire CWhitfield, Eleanor JApweiler, RolfKoyanagi, Kanako OKhurana, Jitendra PRaghuvanshi, SaurabhSingh, Nagendra KTyagi, Akhilesh KHaberer, GeorgFujisawa, MasakiHosokawa, SatomiIto, YukiyoIkawa, HiroshiShibata, MichieYamamoto, MayuBruskiewich, Richard MHoen, Douglas RBureau, Thomas ENamiki, NobukazuOhyanagi, HajimeSakai, YasumichiNobushima, SatoshiSakata, KatsumiBarrero, Roberto ASato, YutakaSouvorov, AlexandreSmith-White, BrianTatusova, TatianaAn, SuyoungAn, GynheungOOta, SatoshiFuks, GalinaMessing, JoachimChristie, Karen RLieberherr, DamienKim, HyeRanZuccolo, AndreaWing, Rod ANobuta, KanGreen, Pamela JLu, ChengMeyers, Blake CChaparro, CristianPiegu, BenoitPanaud, OlivierEcheverria, ManuelResearch Support, Non-U.S. Gov'tEnglandNucleic acids researchNucleic Acids Res. 2008 Jan;36(Database issue):D1028-33. Epub 2007 Dec 17.

Related External URL:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18089549
Citation:
Tanaka, T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T et al..  2008.  The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36:D1028-33.