Literature DB >> 12519938

DNA Data Bank of Japan (DDBJ) in XML.

S Miyazaki1, H Sugawara, T Gojobori, Y Tateno.   

Abstract

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year. This is mainly due to large-scale submissions from Japanese sequencing teams on mouse, rice, chimpanzee, nematoda and other organisms. The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD). Our complete genome sequence database, Genome Information Broker (GIB), has been improved by incorporating XML. It is now possible to perform a more sophisticated database search against the new GIB than the ordinary BLAST or FASTA search.

Entities:  

Mesh：

Year:  2003        PMID： 12519938      PMCID： PMC165535          DOI： 10.1093/nar/gkg088

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


  11 in total

1.  Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.

Authors:  Masaki Fumoto; Satoru Miyazaki; Hideaki Sugawara
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.

Authors:  J D WATSON; F H CRICK
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

3.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

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

Authors:  Y Tateno; T Imanishi; S Miyazaki; K Fukami-Kobayashi; N Saitou; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  DNA Data Bank of Japan at work on genome sequence data.

Authors:  Y Tateno; K Fukami-Kobayashi; S Miyazaki; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

6.  DNA Data Bank of Japan in the age of information biology.

Authors:  Y Tateno; T Gojobori
Journal:  Nucleic Acids Res       Date:  1997-01-01       Impact factor: 16.971

7.  Rapid and sensitive protein similarity searches.

Authors:  D J Lipman; W R Pearson
Journal:  Science       Date:  1985-03-22       Impact factor: 47.728

8.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

9.  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

10.  DNA sequencing with chain-terminating inhibitors.

Authors:  F Sanger; S Nicklen; A R Coulson
Journal:  Proc Natl Acad Sci U S A       Date:  1977-12       Impact factor: 11.205
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  16 in total

1.  DDBJ in the stream of various biological data.

Authors:  S Miyazaki; H Sugawara; K Ikeo; T Gojobori; Y Tateno
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  The EMBL Nucleotide Sequence Database.

Authors:  Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra van den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-Pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle McHale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  IntAct: an open source molecular interaction database.

Authors:  Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; Amos Bairoch; Gianni Cesareni; David Sherman; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.

Authors:  John C Obenauer; Lewis C Cantley; Michael B Yaffe
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  Biological SOAP servers and web services provided by the public sequence data bank.

Authors:  H Sugawara; S Miyazaki
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  GeneSeqer@PlantGDB: Gene structure prediction in plant genomes.

Authors:  Shannon D Schlueter; Qunfeng Dong; Volker Brendel
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

7.  The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

Authors:  Shibu Yooseph; Granger Sutton; Douglas B Rusch; Aaron L Halpern; Shannon J Williamson; Karin Remington; Jonathan A Eisen; Karla B Heidelberg; Gerard Manning; Weizhong Li; Lukasz Jaroszewski; Piotr Cieplak; Christopher S Miller; Huiying Li; Susan T Mashiyama; Marcin P Joachimiak; Christopher van Belle; John-Marc Chandonia; David A Soergel; Yufeng Zhai; Kannan Natarajan; Shaun Lee; Benjamin J Raphael; Vineet Bafna; Robert Friedman; Steven E Brenner; Adam Godzik; David Eisenberg; Jack E Dixon; Susan S Taylor; Robert L Strausberg; Marvin Frazier; J Craig Venter
Journal:  PLoS Biol       Date:  2007-03       Impact factor: 8.029

8.  coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.

Authors:  Roy R Chaudhuri; Arshad M Khan; Mark J Pallen
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  Acidophilic haloarchaeal strains are isolated from various solar salts.

Authors:  Hiroaki Minegishi; Toru Mizuki; Akinobu Echigo; Tadamasa Fukushima; Masahiro Kamekura; Ron Usami
Journal:  Saline Systems       Date:  2008-10-29

10.  Endospores of halophilic bacteria of the family Bacillaceae isolated from non-saline Japanese soil may be transported by Kosa event (Asian dust storm).

Authors:  Akinobu Echigo; Miki Hino; Tadamasa Fukushima; Toru Mizuki; Masahiro Kamekura; Ron Usami
Journal:  Saline Systems       Date:  2005-10-20
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