DDBJ progress report

Eli Kaminuma; Takehide Kosuge; Yuichi Kodama; Hideo Aono; Jun Mashima; Takashi Gojobori; Hideaki Sugawara; Osamu Ogasawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura

doi:10.1093/nar/gkq1041

DDBJ progress report

Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

Abstract

The DNA Data Bank of Japan (DDBJ, http://www .ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3 637 446 entries/2 272 231 889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.

Original language	English (US)
Pages (from-to)	D22-D27
Journal	NUCLEIC ACIDS RESEARCH
Volume	39
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkq1041
State	Published - Jan 2011
Externally published	Yes

Bibliographical note

Funding Information:
Ministry of Education, Culture, Sports, Science and Technology of Japan with a management expense grant for national university cooperation (to DDBJ); Integrated Database Project (http://lifesciencedb.jp/en) of the Database Center for Life Science in Japan (to DDBJ Trace Archive, DDBJ Sequence Read Archive and DDBJ Pipeline, partially); Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (to DDBJ Trace Archive, DDBJ Sequence Read Archive and DDBJ Pipeline, partially). Funding for open access charge: The DDBJ management expenses grant.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkq1041

Cite this

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title = "DDBJ progress report",

abstract = "The DNA Data Bank of Japan (DDBJ, http://www .ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3 637 446 entries/2 272 231 889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.",

author = "Eli Kaminuma and Takehide Kosuge and Yuichi Kodama and Hideo Aono and Jun Mashima and Takashi Gojobori and Hideaki Sugawara and Osamu Ogasawara and Toshihisa Takagi and Kousaku Okubo and Yasukazu Nakamura",

note = "Funding Information: Ministry of Education, Culture, Sports, Science and Technology of Japan with a management expense grant for national university cooperation (to DDBJ); Integrated Database Project (http://lifesciencedb.jp/en) of the Database Center for Life Science in Japan (to DDBJ Trace Archive, DDBJ Sequence Read Archive and DDBJ Pipeline, partially); Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (to DDBJ Trace Archive, DDBJ Sequence Read Archive and DDBJ Pipeline, partially). Funding for open access charge: The DDBJ management expenses grant.",

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AU - Aono, Hideo

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AU - Sugawara, Hideaki

AU - Ogasawara, Osamu

AU - Takagi, Toshihisa

AU - Okubo, Kousaku

AU - Nakamura, Yasukazu

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DDBJ progress report

Abstract

Bibliographical note

ASJC Scopus subject areas

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