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Literature DB >> 11752245

DNA Data Bank of Japan (DDBJ) for genome scale research in life science.

Y Tateno¹, T Imanishi, S Miyazaki, K Fukami-Kobayashi, N Saitou, H Sugawara, T Gojobori.

Abstract

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases. The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale. In addition, we have developed the Genome Information Broker (GIB, http://gib.genes.nig.ac.jp) that now includes more than 50 complete microbial genome and Arabidopsis genome data. We have also developed a database of the human genome, the Human Genomics Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools.

Entities: Species

Mesh：

Year: 2002 PMID： 11752245 PMCID： PMC99140 DOI： 10.1093/nar/30.1.27

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

17 in total

1. The DNA sequence of human chromosome 22.

Authors: I Dunham; N Shimizu; B A Roe; S Chissoe; A R Hunt; J E Collins; R Bruskiewich; D M Beare; M Clamp; L J Smink; R Ainscough; J P Almeida; A Babbage; C Bagguley; J Bailey; K Barlow; K N Bates; O Beasley; C P Bird; S Blakey; A M Bridgeman; D Buck; J Burgess; W D Burrill; K P O'Brien
Journal: Nature Date: 1999-12-02 Impact factor: 49.962

2. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

3. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.

Authors: S Shigenobu; H Watanabe; M Hattori; Y Sakaki; H Ishikawa
Journal: Nature Date: 2000-09-07 Impact factor: 49.962

4. Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA.

Authors: M Shirai; H Hirakawa; M Kimoto; M Tabuchi; F Kishi; K Ouchi; T Shiba; K Ishii; M Hattori; S Kuhara; T Nakazawa
Journal: Nucleic Acids Res Date: 2000-06-15 Impact factor: 16.971

5. Whole genome sequencing of meticillin-resistant Staphylococcus aureus.

Authors: M Kuroda; T Ohta; I Uchiyama; T Baba; H Yuzawa; I Kobayashi; L Cui; A Oguchi; K Aoki; Y Nagai; J Lian; T Ito; M Kanamori; H Matsumaru; A Maruyama; H Murakami; A Hosoyama; Y Mizutani-Ui; N K Takahashi; T Sawano; R Inoue; C Kaito; K Sekimizu; H Hirakawa; S Kuhara; S Goto; J Yabuzaki; M Kanehisa; A Yamashita; K Oshima; K Furuya; C Yoshino; T Shiba; M Hattori; N Ogasawara; H Hayashi; K Hiramatsu
Journal: Lancet Date: 2001-04-21 Impact factor: 79.321

6. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

Authors: S Tabata; T Kaneko; Y Nakamura; H Kotani; T Kato; E Asamizu; N Miyajima; S Sasamoto; T Kimura; T Hosouchi; K Kawashima; M Kohara; M Matsumoto; A Matsuno; A Muraki; S Nakayama; N Nakazaki; K Naruo; S Okumura; S Shinpo; C Takeuchi; T Wada; A Watanabe; M Yamada; M Yasuda; S Sato; M de la Bastide; E Huang; L Spiegel; L Gnoj; A O'Shaughnessy; R Preston; K Habermann; J Murray; D Johnson; T Rohlfing; J Nelson; T Stoneking; K Pepin; J Spieth; M Sekhon; J Armstrong; M Becker; E Belter; H Cordum; M Cordes; L Courtney; W Courtney; M Dante; H Du; J Edwards; J Fryman; B Haakensen; E Lamar; P Latreille; S Leonard; R Meyer; E Mulvaney; P Ozersky; A Riley; C Strowmatt; C Wagner-McPherson; A Wollam; M Yoakum; M Bell; N Dedhia; L Parnell; R Shah; M Rodriguez; L H See; D Vil; J Baker; K Kirchoff; K Toth; L King; A Bahret; B Miller; M Marra; R Martienssen; W R McCombie; R K Wilson; G Murphy; I Bancroft; G Volckaert; R Wambutt; A Düsterhöft; W Stiekema; T Pohl; K D Entian; N Terryn; N Hartley; E Bent; S Johnson; S A Langham; B McCullagh; J Robben; B Grymonprez; W Zimmermann; U Ramsperger; H Wedler; K Balke; E Wedler; S Peters; M van Staveren; W Dirkse; P Mooijman; R K Lankhorst; T Weitzenegger; G Bothe; M Rose; J Hauf; S Berneiser; S Hempel; M Feldpausch; S Lamberth; R Villarroel; J Gielen; W Ardiles; O Bents; K Lemcke; G Kolesov; K Mayer; S Rudd; H Schoof; C Schueller; P Zaccaria; H W Mewes; M Bevan; P Fransz
Journal: Nature Date: 2000-12-14 Impact factor: 49.962

7. Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125.

Authors: K Nakasone; N Masui; Y Takaki; R Sasaki; G Maeno; T Sakiyama; C Hirama; F Fuji; H Takami
Journal: Extremophiles Date: 2000-08 Impact factor: 2.395

8. Functional annotation of a full-length mouse cDNA collection.

Authors: J Kawai; A Shinagawa; K Shibata; M Yoshino; M Itoh; Y Ishii; T Arakawa; A Hara; Y Fukunishi; H Konno; J Adachi; S Fukuda; K Aizawa; M Izawa; K Nishi; H Kiyosawa; S Kondo; I Yamanaka; T Saito; Y Okazaki; T Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; M Ashburner; S Batalov; T Casavant; W Fleischmann; T Gaasterland; C Gissi; B King; H Kochiwa; P Kuehl; S Lewis; Y Matsuo; I Nikaido; G Pesole; J Quackenbush; L M Schriml; F Staubli; R Suzuki; M Tomita; L Wagner; T Washio; K Sakai; T Okido; M Furuno; H Aono; R Baldarelli; G Barsh; J Blake; D Boffelli; N Bojunga; P Carninci; M F de Bonaldo; M J Brownstein; C Bult; C Fletcher; M Fujita; M Gariboldi; S Gustincich; D Hill; M Hofmann; D A Hume; M Kamiya; N H Lee; P Lyons; L Marchionni; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; I Rodriguez; N Sakamoto; H Sasaki; K Sato; C Schönbach; T Seya; Y Shibata; K F Storch; H Suzuki; K Toyo-oka; K H Wang; C Weitz; C Whittaker; L Wilming; A Wynshaw-Boris; K Yoshida; Y Hasegawa; H Kawaji; S Kohtsuki; Y Hayashizaki
Journal: Nature Date: 2001-02-08 Impact factor: 49.962

9. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti.

Authors: T Kaneko; Y Nakamura; S Sato; E Asamizu; T Kato; S Sasamoto; A Watanabe; K Idesawa; A Ishikawa; K Kawashima; T Kimura; Y Kishida; C Kiyokawa; M Kohara; M Matsumoto; A Matsuno; Y Mochizuki; S Nakayama; N Nakazaki; S Shimpo; M Sugimoto; C Takeuchi; M Yamada; S Tabata
Journal: DNA Res Date: 2000-12-31 Impact factor: 4.458

10. The genome sequence of Drosophila melanogaster.

Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

31 in total

1. GenBank: update.

Authors: Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

2. TMPDB: a database of experimentally-characterized transmembrane topologies.

Authors: Masami Ikeda; Masafumi Arai; Toshikatsu Okuno; Toshio Shimizu
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

3. RTKdb: database of Receptor Tyrosine Kinase.

Authors: Julien Grassot; Guy Mouchiroud; Guy Perrière
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

4. DNA Data Bank of Japan (DDBJ) in XML.

Authors: S Miyazaki; H Sugawara; T Gojobori; Y Tateno
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5. The European Bioinformatics Institute's data resources.

Authors: Catherine Brooksbank; Evelyn Camon; Midori A Harris; Michele Magrane; Maria Jesus Martin; Nicola Mulder; Claire O'Donovan; Helen Parkinson; Mary Ann Tuli; Rolf Apweiler; Ewan Birney; Alvis Brazma; Kim Henrick; Rodrigo Lopez; Guenter Stoesser; Peter Stoehr; Graham Cameron
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. GenBank.

Authors: Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

Review 7. An integrated computational pipeline and database to support whole-genome sequence annotation.

Authors: C J Mungall; S Misra; B P Berman; J Carlson; E Frise; N Harris; B Marshall; S Shu; J S Kaminker; S E Prochnik; C D Smith; E Smith; J L Tupy; C Wiel; G M Rubin; S E Lewis
Journal: Genome Biol Date: 2002-12-23 Impact factor: 13.583

8. From phenotype to genotype: issues in navigating the available information resources.

Authors: J A Mitchell; A T McCray; O Bodenreider
Journal: Methods Inf Med Date: 2003 Impact factor: 2.176

9. Computational Epigenetics: the new scientific paradigm.

Authors: Shen Jean Lim; Tin Wee Tan; Joo Chuan Tong
Journal: Bioinformation Date: 2010-01-23

10. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.

Authors: Jessica Severin; Andrew M Waterhouse; Hideya Kawaji; Timo Lassmann; Erik van Nimwegen; Piotr J Balwierz; Michiel Jl de Hoon; David A Hume; Piero Carninci; Yoshihide Hayashizaki; Harukazu Suzuki; Carsten O Daub; Alistair Rr Forrest
Journal: Genome Biol Date: 2009-04-19 Impact factor: 13.583