Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Jan;39(Database issue):D22-7.
doi: 10.1093/nar/gkq1041. Epub 2010 Nov 9.

DDBJ progress report

Eli Kaminuma  1 , Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura
Affiliations

DDBJ progress report

Eli Kaminuma et al. Nucleic Acids Res. 2011 Jan.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Web-based metadata creation tool MetaDefine implemented in DRA submission system.
Figure 2.
Figure 2.
Cloud computing-based NGS analytical tool DDBJ Pipeline. Present running status of all jobs can be viewed in the Status panel.
See this image and copyright information in PMC

References

    1. Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y. DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 2010;38:D33–D38. - PMC - PubMed
    1. Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M. Evidence standards in experimental and inferential INSDC Third Party Annotation data. OMICS. 2006;10:105–113. - PubMed
    1. Shumway M, Cochrane G, Sugawara H. Archiving next generation sequencing data. Nucleic Acids Res. 2010;38:D870–D871. - PMC - PubMed
    1. Rice Annotation Project. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 2008;36:D1028–D1033. - PMC - PubMed
    1. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793–800. - PubMed

Publication types